Affinage

NPLOC4

Nuclear protein localization protein 4 homolog · UniProt Q8TAT6

Length
608 aa
Mass
68.1 kDa
Annotated
2026-06-10
67 papers in source corpus 38 papers cited in narrative 38 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NPLOC4 (Npl4) is the ubiquitin-recognition subunit of the heterodimeric UFD1-NPLOC4 adaptor that directs the AAA+ ATPase p97/VCP to polyubiquitinated substrates, forming an ATP-dependent segregase/unfoldase that extracts ubiquitinated proteins from membranes, chromatin, and protein complexes (PMID:10811609, PMID:11733065, PMID:28512218). NPLOC4 and UFD1 bind p97 as a single heterodimer at the N-D1 plane in a configuration distinct from and mutually exclusive with the p47 adaptor, thereby targeting p97 to ubiquitin-dependent rather than membrane-fusion pathways (PMID:10811609, PMID:17202270). NPLOC4 provides substrate recognition through its zinc-finger (NZF) domain, which binds ubiquitin via a 13TF14 dipeptide engaging the Ile44 surface, and its C-terminal/MPN domain, which contacts both moieties of K48-linked diubiquitin to confer linkage selectivity, while UFD1 adds parallel ubiquitin and SUMO contacts that enable recruitment to STUbL-generated and SUMO-ubiquitin hybrid signals (PMID:12644454, PMID:31836717, PMID:22730331, PMID:36574706). Reconstitution established that p97-NPLOC4-UFD1 is a ubiquitin- and ATP-dependent unfoldase whose activity absolutely requires the adaptor, ATP hydrolysis, and substrate ubiquitination, with branched chains giving maximal stimulation; cryo-EM defined a nucleotide-coupled 'seesaw' motion of the NPLOC4 zinc fingers against the p97 N-domain that is essential for unfolding (PMID:28512218, PMID:33402676, PMID:22232657). This machine is the central post-ubiquitination handler across diverse processes: it acts after substrate ubiquitination in ERAD to liberate and retrotranslocate membrane substrates (PMID:11739805, PMID:12847084, PMID:11733065), disassembles the ubiquitylated CMG helicase to terminate DNA replication (PMID:28355556), degrades cell-cycle and checkpoint regulators such as CDC25A (PMID:24429874), antagonizes Aurora B on mitotic chromosomes (PMID:21486945), clears mislocalized CENP-A/Cse4 from chromatin (PMID:35234920), and extracts stalled nascent chains from the 60S ribosome [PMID:bio_10.1101_2025.01.03.631235]. UBX-domain cofactors including FAF1, FAF2, UBXN7, VCF1/FAM104A, and FAF1 lower the ubiquitin-chain threshold and stabilize productive UFD1-NPLOC4-ubiquitin engagement (PMID:35920641, PMID:38503733, PMID:23293021). NPLOC4 is the cellular target of the disulfiram metabolite CuET, which releases copper that disrupts the NPLOC4 zinc fingers and aggregates the protein, locking the conformational switch and inhibiting p97 segregase function as the basis of disulfiram's anticancer activity (PMID:31391554, PMID:33402676).

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 1996 High

    Before its role in protein degradation was known, Npl4 was identified as a nuclear-envelope-associated factor, raising the question of its core cellular function.

    Evidence Yeast npl4 mutant analysis with nuclear import/export and EM assays

    PMID:8930904

    Open questions at the time
    • Nuclear transport phenotypes were not yet connected to ubiquitin/p97 biology
    • Molecular activity of Npl4 undefined at this stage
  2. 2000 High

    Established that Ufd1-Npl4 is a heterodimeric p97/VCP adaptor that competes with p47, defining how p97 is directed to distinct pathways.

    Evidence Co-IP from rat liver cytosol, competition binding, Golgi fusion assay

    PMID:10811609

    Open questions at the time
    • Did not define substrate range
    • No structural basis for mutual exclusivity
  3. 2001 High

    Defined the Cdc48-Ufd1-Npl4 complex as a ubiquitin-selective segregase acting in ERAD and membrane-bound transcription factor processing, downstream of ubiquitination but before proteasome handoff.

    Evidence Yeast genetics, epistasis, pulse-chase processing/ERAD assays, ubiquitination assays

    PMID:11598205 PMID:11733065 PMID:11739805

    Open questions at the time
    • Mechanism of ubiquitin recognition not yet structural
    • Step between extraction and proteasome unclear
  4. 2003 High

    Reconstituted retrotranslocation and solved the NZF domain structure, showing dual substrate recognition and the molecular basis of weak ubiquitin binding by Npl4.

    Evidence In vitro ER retrotranslocation with ATPase mutants; NMR structure of NZF with ubiquitin-binding mutagenesis

    PMID:12644454 PMID:12847084

    Open questions at the time
    • Linkage selectivity not yet explained
    • Full-length adaptor architecture unresolved
  5. 2007 High

    Determined the architecture of the Ufd1-Npl4 heterodimer on p97 and the Npl4 UBD-p97 N-domain interface, defining adaptor stoichiometry and binding geometry.

    Evidence EM, AUC, SPR, mass spectrometry; NMR of Npl4 UBD and chemical shift mapping

    PMID:17202270 PMID:17491009

    Open questions at the time
    • Conformational dynamics during catalysis not captured
    • Substrate-bound states unknown
  6. 2011 High

    Extended the complex's roles into mitosis, showing Ufd1-Npl4 antagonizes Aurora B on chromosomes to ensure faithful segregation.

    Evidence siRNA, quantitative IF, Aurora B activity assay, chemical epistasis, live imaging in HeLa

    PMID:21486945

    Open questions at the time
    • Whether Aurora B is a direct extraction substrate not established
    • Ubiquitin signal driving recruitment undefined
  7. 2012 High

    Revealed dual SUMO/ubiquitin recognition via a Ufd1 SIM and captured nucleotide-dependent conformational repositioning of the adaptor, linking the machine to STUbL signals and ATPase cycling.

    Evidence Co-IP, SIM mutagenesis, yeast two-hybrid, STUbL epistasis; nucleotide-state cryo-EM

    PMID:22232657 PMID:22730331

    Open questions at the time
    • Cryo-EM conformational model lacked direct mutagenesis validation (Medium)
    • Functional contribution of each conformer unresolved
  8. 2013 Medium

    Mapped the complex onto additional ubiquitin-dependent degradation routes (IκBα/NF-κB, NEDD8) and identified FAF1 as a UBX cofactor that allosterically tunes ubiquitin binding.

    Evidence Co-IP, knockdown, reporter and degradation assays; in vitro binding

    PMID:23293021 PMID:24019527 PMID:24248593

    Open questions at the time
    • Single-lab functional pathways not cross-validated
    • Direct versus indirect substrate engagement unclear for some targets
  9. 2014 Medium

    Connected p97-Ufd1-Npl4 to the G2/M DNA damage checkpoint by handling ubiquitinated CDC25A, establishing a checkpoint-enforcement role.

    Evidence siRNA, Co-IP, cell cycle and CDC25A degradation assays

    PMID:24429874

    Open questions at the time
    • Single lab
    • Whether extraction precedes proteasomal degradation directly not shown
  10. 2017 High

    Defined the fundamental biochemical activity — a ubiquitin- and ATP-dependent unfoldase requiring NPLOC4-UFD1 — and identified CMG helicase disassembly as a chromatin extraction substrate.

    Evidence In vitro reconstituted unfoldase assay with mutants and chain variants; yeast extract CMG disassembly with K29R Mcm7 mapping

    PMID:28355556 PMID:28512218

    Open questions at the time
    • Structural intermediates of unfolding not yet resolved
    • How chain threshold is set in cells unclear
  11. 2019 High

    Provided atomic basis for K48-linkage selectivity and the Ufd1-Npl4 interface, and showed MSP-disease p97 mutants gain tighter adaptor binding and faster unfolding.

    Evidence Crystal structures of Npl4-K48-diUb and Npl4-Ufd1; cryo-EM and in vitro unfoldase assays of seven MSP mutants

    PMID:31623962 PMID:31836717

    Open questions at the time
    • Physiological consequence of gain-of-function in patient tissues not addressed here
    • Full substrate path through the pore not visualized
  12. 2019 High

    Identified NPLOC4 as the direct cellular target of the disulfiram metabolite CuET, explaining its anticancer mechanism through p97 segregase inhibition.

    Evidence Cell viability, ALDH negative control, NPL4 aggregation and ubiquitin accumulation assays

    PMID:31391554

    Open questions at the time
    • Molecular mechanism of aggregation not yet defined (addressed later)
    • In vivo selectivity window not detailed
  13. 2021 High

    Resolved the 'seesaw' conformational states of NPLOC4 zinc fingers against the p97 N-domain as essential for unfolding, and showed CuET-released copper disrupts these zinc fingers to lock the switch.

    Evidence Cryo-EM, in vitro unfolding assays, copper transporter bypass, zinc finger disruption

    PMID:33402676

    Open questions at the time
    • Kinetics of conformer transitions during processive unfolding not measured
    • Generality of seesaw across substrate classes untested
  14. 2022 High

    Defined a high ubiquitin-chain threshold relieved by UBX cofactors, demonstrated SUMO enhancement of unfolding, and provided human-complex crystal and integrative structures.

    Evidence Reconstituted CMG disassembly with UBXN7/FAF1/FAF2; SUMO-Ub unfolding and cryo-EM; X-ray of hUN; XL-MS integrative model with C115S validation

    PMID:18586029 PMID:35920641 PMID:36087575 PMID:36574706 PMID:37311459

    Open questions at the time
    • Cofactor selection logic across pathways unclear
    • How threshold is regulated in different compartments unresolved
  15. 2022 Medium

    Broadened substrate scope to chromatin quality control (mislocalized Cse4/CENP-A) and to viral hijacking (flavivirus NS4B recruitment for replication and stress granule disassembly).

    Evidence Yeast ts mutants, ChIP, Co-IP, ubiquitination, epistasis; siRNA rescue with VCP cofactor mutants and replication assays

    PMID:35063505 PMID:35234920

    Open questions at the time
    • Viral mechanism from single lab
    • Direct extraction of Cse4 versus indirect effect not fully separated
  16. 2024 Medium

    Identified additional cofactors (VCF1/FAM104A) and immune-regulatory substrate routes (STAT3 degradation in Tregs; RIG-I degradation in macrophages), linking the segregase to antitumor immunity.

    Evidence Co-IP, binding and degradation assays, knockouts, in vivo tumor and macrophage polarization models

    PMID:38503733 PMID:39107403 PMID:41800259

    Open questions at the time
    • Immune substrate routes from single labs
    • Whether STAT3/RIG-I require physical unfolding versus adaptor scaffolding unclear
  17. 2025 Low

    Emerging structural work places NPLOC4-containing p97 directly coupled to the 20S proteasome and within the ribosome quality control extraction complex, and details FAF1's mechanism of stimulating initiator-ubiquitin engagement.

    Evidence In situ cryo-ET, cryo-EM of RQC, reconstituted unfoldase and FRET assays (all preprints)

    PMID:bio_10.1101_2025.01.03.631235 PMID:bio_10.1101_2025.04.01.646186 PMID:bio_10.1101_2025.10.27.684972

    Open questions at the time
    • Preprints not peer-reviewed; NPLOC4 density inferred in some cases
    • Direct substrate handoff to 20S not validated by mutagenesis

Open questions

Synthesis pass · forward-looking unresolved questions
  • How NPLOC4 selects among its many pathways in a given cellular context, and how cofactor and chain-threshold logic is coordinated in vivo, remains unresolved.
  • No unified model of pathway-specific recruitment
  • In vivo regulation of conformational dynamics not measured
  • Relationship between nuclear-transport phenotype and segregase role unexplained

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0140657 ATP-dependent activity 3 GO:0098772 molecular function regulator activity 2
Localization
GO:0005783 endoplasmic reticulum 3 GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2 GO:0005829 cytosol 2 GO:0005635 nuclear envelope 1
Pathway
R-HSA-168256 Immune System 3 R-HSA-392499 Metabolism of proteins 3 R-HSA-1640170 Cell Cycle 2 R-HSA-69306 DNA Replication 2 R-HSA-73894 DNA Repair 1 R-HSA-8953854 Metabolism of RNA 1
Partners
FAF1FAF2FAM104ANUB1LSUMOUBXN7UFD1VCP
Complex memberships
Cdc48-Ufd1-Npl4 complexp97-UFD1-NPLOC4 segregase

Evidence

Reading pass · 38 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 Mammalian Ufd1 and Npl4 form a binary heterodimer that associates with p97/VCP; the Ufd1-Npl4 complex competes with p47 for binding to p97 and thus inhibits Golgi membrane fusion, indicating that Ufd1-Npl4 and p47 are mutually exclusive adaptors that direct p97 to distinct cellular pathways. Co-immunoprecipitation from rat liver cytosol; competition binding assay with recombinant proteins; Golgi membrane fusion assay The EMBO journal High 10811609
2001 In yeast, the Cdc48(UFD1/NPL4) complex acts as a ubiquitin-selective chaperone/segregase that liberates the processed, ubiquitinated transcription factor Spt23 (p90) from its unprocessed ER-membrane-bound partner to allow nuclear targeting; the complex preferentially binds ubiquitinated substrates. Yeast genetics (mutant analysis), co-immunoprecipitation, in vivo ubiquitination assay, subcellular fractionation Cell High 11733065
2001 In yeast, Npl4p, Ufd1p, and Cdc48p form a membrane-associated complex required for proteasome-regulated cleavage of membrane-bound transcription factors Mga2p and Spt23p; mutations in any member block processing and abolish OLE1 expression. Yeast genetic epistasis (npl4, ufd1, cdc48 temperature-sensitive mutants), reporter gene assays, pulse-chase protein processing assay Molecular biology of the cell High 11598205
2001 HRD4/NPL4 (yeast) is required for ERAD at a step after substrate ubiquitination but before recognition by the 26S proteasome; each member of the Cdc48p-Ufd1p-Npl4p complex is individually required for this function. Yeast temperature-sensitive mutant analysis (hrd4/npl4), pulse-chase ERAD assays with diverse substrates, direct ubiquitination assays Molecular biology of the cell High 11739805
2002 Cdc48(UFD1/NPL4) functions as a segregase that mediates ERAD of OLE1, demonstrating a constitutive role in ERAD beyond SPT23 processing; it liberates ubiquitylated proteins from non-modified protein partners. Yeast genetics, pulse-chase degradation assays, co-immunoprecipitation The EMBO journal High 11847109
2003 The p97-Ufd1-Npl4 complex drives retrotranslocation via dual substrate recognition: (1) the p97 ATPase itself binds non-ubiquitinated polypeptide segments emerging from the ER membrane; (2) Lys48-linked polyubiquitin chains are synergistically recognized by p97 and a conserved N-terminal ubiquitin-binding site of Ufd1. Substrate binding requires the D1 domain of p97 in its nucleotide-bound state and membrane association through the p97 NH2-terminal domain; alternating ATP hydrolysis by D1 and D2 domains is essential for polypeptide movement. In vitro retrotranslocation assay with ER membranes and purified components; ATPase mutant analysis; co-immunoprecipitation; nucleotide-state binding assays The Journal of cell biology High 12847084
2003 The Npl4 zinc finger (NZF) domain adopts a compact four-antiparallel-beta-strand module with a zinc ion coordinated by four cysteines in two rubredoxin knuckles; it binds specifically but weakly to free ubiquitin via a conserved 13TF14 dipeptide interacting with the Ile44 surface of ubiquitin. NMR solution structure determination; ubiquitin binding assays (NMR, isothermal titration calorimetry); mutagenesis of the TF dipeptide The Journal of biological chemistry High 12644454
2005 The p97-Ufd1-Npl4 complex associates with ubiquitinated IP3 receptors at the ER in mammalian cells upon hormonal stimulation and is required for their proteasomal degradation; RNAi knockdown of p97 retards IP3 receptor degradation and increases ubiquitinated receptor accumulation. Co-immunoprecipitation from mammalian cells; RNA interference of p97; pulse-chase degradation assay; rescue by exogenous p97 expression The Journal of biological chemistry High 16103111
2007 The Ufd1-Npl4 heterodimer has an elongated bilobed structure (~80×30 Å); one Ufd1-Npl4 heterodimer binds one p97 hexamer at the periphery of the N-D1 plane, in a configuration distinct from the p97-p47 complex in stoichiometry, symmetry, and quaternary arrangement. Electron microscopy; mass spectrometry; analytical ultracentrifugation; surface plasmon resonance Proceedings of the National Academy of Sciences of the United States of America High 17202270
2007 The Npl4 ubiquitin-like domain (UBD) adopts a beta-grasp fold with a 3(10) helical insert and binds the p97 N-domain via a defined surface; Ufd1 binds a separate surface of the p97 N-domain; together these interactions define the structural basis of p97-UN adaptor specificity. NMR solution structure of Npl4 UBD; NMR chemical shift perturbation mapping of p97 N-domain binding surface; structural model of the p97 N–Npl4 UBD complex The Journal of biological chemistry High 17491009
2011 In HeLa cells, Ufd1-Npl4 antagonizes Aurora B kinase on chromosomes during prometaphase and metaphase; siRNA depletion of Ufd1-Npl4 increases Aurora B levels and activity on chromosomes, causing chromosome alignment and anaphase defects, missegregation, and multi-lobed nuclei. siRNA knockdown; quantitative immunofluorescence; Aurora B activity assay (CENP-A phosphorylation); chemical epistasis with Aurora B inhibitor hesperadin; live-cell imaging Journal of cell science High 21486945
2012 The Cdc48-Ufd1-Npl4 'ubiquitin-selective' segregase also binds SUMO via a SUMO interaction motif in Ufd1, enabling dual recruitment by both SUMO and ubiquitin signals generated by SUMO-targeted ubiquitin ligases (STUbLs); this mechanism is important for genome stability functions. Co-immunoprecipitation; SUMO interaction motif identification and mutagenesis; yeast two-hybrid; genetic epistasis with STUbL mutants The Journal of biological chemistry High 22730331
2012 Cryo-EM reveals that p97-Ufd1-Npl4 is highly dynamic; Ufd1-Npl4 assumes distinct positions relative to the p97 ring dependent on nucleotide state, suggesting a model for substrate remodeling coupled to p97 ATPase cycling. Single-particle cryo-electron microscopy reconstruction in different nucleotide states Proceedings of the National Academy of Sciences of the United States of America Medium 22232657
2013 FAF1 interacts with the VCP-Npl4-Ufd1 complex specifically (not VCP alone) via its UBX domain; this interaction allosterically regulates ubiquitin binding to FAF1's UBA domain, promoting ERAD of polyubiquitinated substrates. Co-immunoprecipitation; structural analysis; in vitro binding assays; ERAD substrate degradation assays in cells The Journal of biological chemistry Medium 23293021
2013 The p97-UFD1L-NPL4 complex mediates cytokine-induced IκBα proteolysis; it binds ubiquitinated IκBα through UFD1L's polyubiquitin-binding domain and through p97's interaction with SCF-βTrCP ubiquitin ligase, and this is required for NF-κB activation after TNF-α or IL-1β treatment. Co-immunoprecipitation; siRNA knockdown; NF-κB reporter assay; IκBα degradation assay; ATPase-dead p97 mutant Molecular and cellular biology Medium 24248593
2014 p97-Ufd1-Npl4 is required for the G2/M DNA damage checkpoint by binding ubiquitinated CDC25A downstream of SCF-βTrCP ubiquitination and facilitating its proteasomal degradation; Ufd1-Npl4 depletion causes G2/M checkpoint failure with persistent CDC25A activity and propagation of DNA damage into mitosis. siRNA depletion; co-immunoprecipitation; cell cycle analysis; DNA damage assays; CDC25A degradation assay Cell cycle (Georgetown, Tex.) Medium 24429874
2017 p97-NPLOC4-UFD1L is a ubiquitin- and ATP-dependent protein unfoldase; wild-type p97 can unfold a model substrate (Ub-GFP with K48-linked chains) in vitro, and this activity absolutely requires NPLOC4-UFD1L, ATP hydrolysis, and substrate ubiquitination; branched ubiquitin chains provide maximal stimulation; an MSP-causing p97 mutant unfolds substrate faster. In vitro unfoldase assay with purified components; ATPase mutants; ubiquitin chain linkage variants; fluorescence-based unfolding readout Proceedings of the National Academy of Sciences of the United States of America High 28512218
2017 The ubiquitin-binding Ufd1-Npl4 complex recruits Cdc48 to ubiquitylated CMG helicase (via Mcm7 K29 ubiquitylation) to drive its disassembly at the end of chromosome replication; mutation of K29 abrogates Ufd1-Npl4-Cdc48 recruitment to CMG. Yeast cell-free extract CMG disassembly assay; ubiquitin site mapping by mass spectrometry; K29R Mcm7 mutant; Co-immunoprecipitation Cell reports High 28355556
2019 Crystal structures of yeast Npl4 in complex with K48-linked diubiquitin reveal that the Npl4 C-terminal domain (CTD) contacts both distal (via C-terminal helix) and proximal (via N-terminal loop) ubiquitin moieties; the CTD contributes to K48-linkage selectivity; Ufd1 binds a hydrophobic groove in the MPN domain of Npl4 corresponding to the catalytic groove of JAMM-family DUBs. X-ray crystallography (crystal structures of Npl4–K48-diUb and Npl4–Ufd1 peptide); site-directed mutagenesis; in vitro binding assays Nature communications High 31836717
2019 MSP-causing p97 mutants show tighter binding to the NPLOC4-UFD1L adaptor and faster substrate unfolding; cryo-EM structural analysis suggests that increased UN affinity originates from decoupling of p97 nucleotide state and N-terminal domain positioning; all seven analyzed MSP mutants share these gain-of-function properties. Cryo-EM structure determination; in vitro unfoldase assays with purified components; quantitative binding assays; panel of seven MSP mutant p97 homo- and heterohexamers Structure (London, England : 1993) High 31623962
2019 The anticancer activity of disulfiram operates through its copper-containing metabolite CuET, which causes aggregation of NPL4, a subunit of the p97/VCP segregase, rather than through ALDH inhibition; NPL4 aggregation by CuET impairs p97 segregase function and kills cancer cells. Cell viability assays; ALDH activity assays; NPL4 aggregation assay; ubiquitinated protein accumulation; BRCA1/2-deficient cell sensitivity comparison; CuET versus DSF metabolite comparison Oncogene High 31391554
2021 Cryo-EM reveals three Npl4 conformational states in complex with human p97 before ATP hydrolysis ('seesaw' conformations); motion of Npl4 is driven by its zinc finger motifs interacting with the N-domain of p97 and is essential for p97 unfolding activity; CuET releases cupric ions under oxidative conditions that disrupt Npl4 zinc finger motifs, locking the conformational switch and inhibiting p97 function. Single-particle cryo-EM; in vitro p97 unfolding activity assay; cell-based copper transporter bypass experiments; zinc finger disruption assays Nature communications High 33402676
2022 SUMO modifications on substrates enhance Ufd1/Npl4/Cdc48-mediated unfolding compared to polyubiquitin alone; SUMO interacts with Ufd1 to augment this activity; cryo-EM structures of the complex with SUMO-polyubiquitin-modified substrate reveal interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding. In vitro reconstituted unfolding assay with SUMO-Ub hybrid chains vs. Ub alone; cryo-EM structure determination; competition assay; Ufd1-SUMO interaction mapping Proceedings of the National Academy of Sciences of the United States of America High 36574706
2022 Mammalian p97-UFD1-NPL4 has a high ubiquitin-chain threshold for substrate unfolding that is reduced by UBX proteins UBXN7, FAF1, or FAF2; these UBX proteins bind p97-UFD1-NPL4 and stabilize productive interactions between UFD1-NPL4 and K48-linked chains of at least five ubiquitins; FAF1 and FAF2 use a previously uncharacterized coiled-coil domain for this stimulation. Reconstituted in vitro CMG disassembly assay; quantitative ubiquitin chain binding assays; mutagenesis of ubiquitin-binding motifs; UBXN7/FAF1 knockout cell lines; S-phase and mitosis CMG disassembly assays eLife High 35920641
2022 Cdc48-Ufd1-Npl4 segregase facilitates removal of polyubiquitinated mislocalized Cse4/CENP-A from non-centromeric chromatin; Npl4 (ubiquitin-binding receptor) associates with mislocalized Cse4 in a manner dependent on Psh1-mediated polyubiquitination. Yeast genetics (cdc48, ufd1, npl4 temperature-sensitive mutants); chromatin immunoprecipitation; co-immunoprecipitation; ubiquitination assays; psh1Δ epistasis Nucleic acids research High 35234920
2022 Flavivirus NS4B protein directly interacts with NPL4 and recruits the VCP-NPL4 complex to viral replication sites; NPL4 depletion impairs early viral genome replication; the VCP-NPL4 interaction is required for stress granule disassembly that facilitates viral protein synthesis. siRNA rescue with VCP cofactor interaction mutants; Co-immunoprecipitation; confocal microscopy localization; stress granule assay; viral replication assay The Journal of biological chemistry Medium 35063505
2022 Binding of Ufd1 to Npl4 is mediated by two regions: a conserved stretch (aa 113-255) within the zf-Npl4 domain and the Npl4 homology domain (aa 263-344); within the first region, discrete subdomains mediate Ufd1 binding and regulate VCP binding separately. Deletion mutant series expressed in mammalian cells; co-immunoprecipitation; ER/Golgi morphology analysis; ER stress assay (BiP/GRP74 induction) Experimental cell research Medium 18586029
2022 Crystal structure of the human Ufd1-Npl4 (UN) complex at 2.7 Å resolution reveals atomic details of the hUfd1–hNpl4 interface; site-directed mutagenesis of hUfd1 residues in the interaction surface validates the structural model. X-ray crystallography of hNpl4 alone (3.0 Å) and hUN complex (2.7 Å); site-directed mutagenesis of interface residues; binding assays Structure (London, England : 1993) High 36087575
2023 Integrative structural modeling (crosslinking mass spectrometry + subunit structures) of the Cdc48-Npl4-Ufd1 ternary complex reveals that binding to the Cdc48 NTD stabilizes the UN assembly; a conserved cysteine C115 at the Cdc48-NTD–Npl4 interface is central to complex stability; C115S mutation disrupts the Cdc48-NTD–Npl4-Ufd1 interaction and causes moderate growth defects and impaired protein quality control. Crosslinking mass spectrometry; integrative structural modeling; site-directed mutagenesis (C115S); yeast growth assays; protein quality control assays Structure (London, England : 1993) Medium 37311459
2024 The p97-Npl4 complex bridges STAT3 with E3 ligases PDLIM2 and PDLIM5, promoting STAT3 degradation and thereby enabling tumor-infiltrating regulatory T (TI-Treg) cell development; pharmacological disruption of p97-Npl4 interaction with thonzonium bromide boosts antitumor immunity. Co-immunoprecipitation; STAT3 ubiquitination and degradation assay; thonzonium bromide binding assay; genetic knockout; in vivo tumor models; Treg/TH17 balance assessment Nature immunology Medium 39107403
2024 VCF1/FAM104A acts as a p97 cofactor that engages in joint complex formation with UFD1-NPL4 and indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 (not through intrinsic ubiquitin affinity), promoting p97-UFD1-NPL4-dependent proteasomal degradation. Co-immunoprecipitation; quantitative binding assays; ubiquitin binding assays; proteasomal degradation assays in cells; structure-function mutagenesis of VCF1 Nature communications High 38503733
2024 NPLOC4 knockdown in oxidative stress conditions reduces VCP recruitment to non-cytosolic compartments, establishing that VCP recruitment to these compartments under arsenite stress is mediated by its NPLOC4 adaptor; VCP and NPLOC4 activities sustain low levels of non-cytosolic K63-linked ubiquitin chains. Subcellular fractionation; ubiquitin proteomics; siRNA knockdown; K63-ubiquitin chain quantification by mass spectrometry bioRxiv (preprint)preprint Medium bio_10.1101_2024.06.20.598218
2025 FAF1 accelerates p97-NPLOC4-UFD1L-dependent substrate unfolding by promoting engagement and unfolding of an initiator ubiquitin; FAF1 uses its p97-bound C-terminal UBX domain to anchor a long helix that braces the UT3 domain of Ufd1, stabilizing the Ufd1-Npl4 cofactor for ubiquitin unfolding. In vitro reconstituted unfoldase assay with human components; cryo-EM structure determination; FRET-based unfolding assay; domain mutagenesis bioRxiv (preprint)preprint Medium bio_10.1101_2025.10.27.684972
2025 Cryo-EM of VCP/p97 at polyQ aggregates in situ shows VCP predominantly in ATP-bound active processing conformation with resolved NPLOC4-like cofactor density, and directly coupled to the 20S proteasome via VCP's C-terminal HbYX motif, suggesting NPLOC4-containing VCP complex hands off substrates directly to the 20S. In situ cryo-electron tomography and subtomogram averaging; cryo-EM single-particle analysis; in vitro HbYX-20S binding assays bioRxiv (preprint)preprint Low bio_10.1101_2025.04.01.646186
2025 Cryo-EM structure of the RQC complex shows that the Cdc48 (p97) extractase with Ufd1-Npl4 adaptor is recruited by the Ltn1 E3 ubiquitin ligase to extract K48-polyubiquitylated stalled nascent chains from the 60S ribosome; Rqc1 bridges the 60S ribosome with ubiquitin and Ltn1 to facilitate K48-linked chain formation on stalled peptides. Cryo-EM structure of budding yeast RQC complex; biochemical reconstitution; ubiquitin linkage analysis bioRxiv (preprint)preprint Low bio_10.1101_2025.01.03.631235
1996 Yeast Npl4p is required for nuclear protein import and mRNA export; npl4 mutant cells accumulate nuclear-targeted proteins in the cytoplasm and poly(A)+ RNA in the nucleus at non-permissive temperature; Npl4p localizes to the nuclear periphery in a pattern similar to nuclear pore complex proteins; npl4 mutations cause distinct nuclear envelope structural defects (extra NE projections or herniations). Yeast genetic mutant analysis (npl4-1, npl4-2); in vitro nuclear import assay; fluorescence microscopy localization; poly(A)+ RNA in situ hybridization; electron microscopy of nuclear envelope Molecular biology of the cell High 8930904
2013 NUB1L promotes NEDD8/neddylation degradation via the P97-UFD1-NPL4 complex; NUB1L directly interacts with NEDD8 (on residue Asn-51) and with P97/VCP, and in coordination with the P97-UFD1-NPL4 complex facilitates NEDD8 transfer to the proteasome for degradation. Co-immunoprecipitation; in vitro binding assay; point mutagenesis (NEDD8 Asn-51); NEDD8/neddylation level assays; proteasomal degradation assay The Journal of biological chemistry Medium 24019527
2024 NPLOC4 binds to RIG-I in tumor-associated macrophages and mediates its ubiquitination-dependent proteasomal degradation, thereby suppressing the type I interferon pathway and promoting M2 macrophage polarization; NPLOC4 inhibition reverses this immunosuppression. Co-immunoprecipitation; ubiquitination assay; proteasome inhibitor experiment; in vitro/in vivo macrophage polarization assays; interferon pathway reporter assays International journal of biological sciences Medium 41800259

Source papers

Stage 0 corpus · 67 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2003 Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. The Journal of cell biology 505 12847084
2000 A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways. The EMBO journal 385 10811609
2001 Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 372 11733065
2002 Role of the ubiquitin-selective CDC48(UFD1/NPL4 )chaperone (segregase) in ERAD of OLE1 and other substrates. The EMBO journal 278 11847109
2001 HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Molecular biology of the cell 249 11739805
2017 Ubiquitin- and ATP-dependent unfoldase activity of P97/VCP•NPLOC4•UFD1L is enhanced by a mutation that causes multisystem proteinopathy. Proceedings of the National Academy of Sciences of the United States of America 154 28512218
2001 The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation. Molecular biology of the cell 134 11598205
2002 Cdc48-Ufd1-Npl4: stuck in the middle with Ub. Current biology : CB 132 12015140
2003 Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4. The Journal of biological chemistry 131 12644454
2019 Disulfiram's anti-cancer activity reflects targeting NPL4, not inhibition of aldehyde dehydrogenase. Oncogene 98 31391554
2011 Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proceedings of the National Academy of Sciences of the United States of America 92 22139374
2021 Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative. Nature communications 89 33402676
2007 Structural insights into the p97-Ufd1-Npl4 complex. Proceedings of the National Academy of Sciences of the United States of America 81 17202270
2012 Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 ubiquitin-selective segregase by small ubiquitin-like modifier protein (SUMO) and ubiquitin in SUMO-targeted ubiquitin ligase-mediated genome stability functions. The Journal of biological chemistry 75 22730331
2019 Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Structure (London, England : 1993) 58 31623962
1996 Nuclear transport defects and nuclear envelope alterations are associated with mutation of the Saccharomyces cerevisiae NPL4 gene. Molecular biology of the cell 57 8930904
2007 Detailed structural insights into the p97-Npl4-Ufd1 interface. The Journal of biological chemistry 55 17491009
2013 Complex of Fas-associated factor 1 (FAF1) with valosin-containing protein (VCP)-Npl4-Ufd1 and polyubiquitinated proteins promotes endoplasmic reticulum-associated degradation (ERAD). The Journal of biological chemistry 53 23293021
2011 Cdc48/p97-Ufd1-Npl4 antagonizes Aurora B during chromosome segregation in HeLa cells. Journal of cell science 49 21486945
2022 Disulfiram/Copper induces antitumor activity against gastric cancer via the ROS/MAPK and NPL4 pathways. Bioengineered 47 35290151
2005 Involvement of the p97-Ufd1-Npl4 complex in the regulated endoplasmic reticulum-associated degradation of inositol 1,4,5-trisphosphate receptors. The Journal of biological chemistry 44 16103111
2019 Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Nature communications 40 31836717
2017 Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication. Cell reports 40 28355556
2012 Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy. Proceedings of the National Academy of Sciences of the United States of America 40 22232657
2013 The p97-UFD1L-NPL4 protein complex mediates cytokine-induced IκBα proteolysis. Molecular and cellular biology 39 24248593
2020 Targeting the NPL4 Adaptor of p97/VCP Segregase by Disulfiram as an Emerging Cancer Vulnerability Evokes Replication Stress and DNA Damage while Silencing the ATR Pathway. Cells 38 32085572
2015 Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nature communications 36 26365526
2019 A commonly occurring genetic variant within the NPLOC4-TSPAN10-PDE6G gene cluster is associated with the risk of strabismus. Human genetics 35 31073882
2015 Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast. Nature communications 35 26537787
2006 Destabilization of the VCP-Ufd1-Npl4 complex is associated with decreased levels of ERAD substrates. Experimental cell research 34 16822501
2022 Anticancer effects of disulfiram in T-cell malignancies through NPL4-mediated ubiquitin-proteasome pathway. Journal of leukocyte biology 29 35363385
2010 The p97 ATPase dislocates MHC class I heavy chain in US2-expressing cells via a Ufd1-Npl4-independent mechanism. The Journal of biological chemistry 27 20702414
2020 Targeting NPL4 via drug repositioning using disulfiram for the treatment of clear cell renal cell carcinoma. PloS one 26 32667929
2016 Differential Involvement of the Npl4 Zinc Finger Domains of SHARPIN and HOIL-1L in Linear Ubiquitin Chain Assembly Complex-Mediated Cell Death Protection. Molecular and cellular biology 24 26976635
2007 The AAA-ATPase p97-Ufd1-Npl4 is required for ERAD but not for spindle disassembly in Xenopus egg extracts. Journal of cell science 24 17374636
2022 Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase. eLife 23 35920641
2013 NEDD8 ultimate buster-1 long (NUB1L) protein promotes transfer of NEDD8 to proteasome for degradation through the P97UFD1/NPL4 complex. The Journal of biological chemistry 23 24019527
2022 SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proceedings of the National Academy of Sciences of the United States of America 20 36574706
2022 Flavivirus recruits the valosin-containing protein-NPL4 complex to induce stress granule disassembly for efficient viral genome replication. The Journal of biological chemistry 19 35063505
2024 Targeting p97-Npl4 interaction inhibits tumor Treg cell development to enhance tumor immunity. Nature immunology 18 39107403
2022 Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin. Nucleic acids research 16 35234920
2004 The Cdc48/p97-Ufd1-Npl4 complex: its potential role in coordinating cellular morphogenesis during the M-G1 transition. Cell cycle (Georgetown, Tex.) 16 15004522
2023 Overcoming the compensatory increase in NRF2 induced by NPL4 inhibition enhances disulfiram/copper-induced oxidative stress and ferroptosis in renal cell carcinoma. European journal of pharmacology 15 37838104
2021 Disulfiram and copper combination therapy targets NPL4, cancer stem cells and extends survival in a medulloblastoma model. PloS one 15 34731160
2014 The p97-Ufd1-Npl4 ATPase complex ensures robustness of the G2/M checkpoint by facilitating CDC25A degradation. Cell cycle (Georgetown, Tex.) 15 24429874
2010 The Cdc48-Ufd1-Npl4 complex is central in ubiquitin-proteasome triggered catabolite degradation of fructose-1,6-bisphosphatase. Biochemical and biophysical research communications 13 20206597
2022 The p97-Nploc4 ATPase complex plays a role in muscle atrophy during cancer and amyotrophic lateral sclerosis. Journal of cachexia, sarcopenia and muscle 12 35611892
2019 Upregulation of NPL4 promotes bladder cancer cell proliferation by inhibiting DXO destabilization of cyclin D1 mRNA. Cancer cell international 12 31164795
2017 Roles for the VCP co-factors Npl4 and Ufd1 in neuronal function in Drosophila melanogaster. Journal of genetics and genomics = Yi chuan xue bao 12 29037990
2016 Evaluating p97 Inhibitor Analogues for Potency against p97-p37 and p97-Npl4-Ufd1 Complexes. ChemMedChem 12 27043824
2011 Cdc48 and cofactors Npl4-Ufd1 are important for G1 progression during heat stress by maintaining cell wall integrity in Saccharomyces cerevisiae. PloS one 12 21526151
2008 Analysis of Npl4 deletion mutants in mammalian cells unravels new Ufd1-interacting motifs and suggests a regulatory role of Npl4 in ERAD. Experimental cell research 12 18586029
2009 Ssz1 restores endoplasmic reticulum-associated protein degradation in cells expressing defective cdc48-ufd1-npl4 complex by upregulating cdc48. Genetics 11 20038635
2022 Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Structure (London, England : 1993) 8 36087575
2001 Cloning and characterization of the gene encoding human NPL4, a protein interacting with the ubiquitin fusion-degradation protein (UFD1L). Gene 7 11574150
2024 VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates. Nature communications 6 38503733
2024 NPLOC4 aggravates heart failure by regulating ROS and mitochondrial function. International immunopharmacology 6 39332095
2024 Trim21 modulates endoplasmic reticulum-associated degradation and sensitizes cancer cells to ER stress-induced apoptosis by inhibiting VCP/Npl4/UFD1 assembly. Biochimica et biophysica acta. Molecular basis of disease 4 39368714
2023 Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy. Biochimica et biophysica acta. Proteins and proteomics 4 37230374
2023 Identification of novel dithiocarbamate-copper complexes targeting p97/NPL4 pathway in cancer cells. European journal of medicinal chemistry 4 37690264
2023 The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation. Structure (London, England : 1993) 3 37311459
2025 [64Cu]Cu(DDC)2 NPs: A Novel PET Probe for Noninvasive Visualization of NPL4 Expression in Tumors In Vivo. Molecular pharmaceutics 1 39927715
2025 A novel feedback regulation loop of METTL11A-MAFG-NPL4 promotes bladder cancer cell proliferation and tumor progression. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1 40171788
2025 FERONIA interacts with NPL4 to regulate immunity gene mRNA nucleocytoplasmic transport in response to plant immunity. Plant science : an international journal of experimental plant biology 1 40348341
2026 NPLOC4 Inhibition Remodels Tumor Microenvironment via M2-to-M1 Macrophage Reprogramming and Boosts Anti-PD-1 Response in Liver Cancer. International journal of biological sciences 0 41800259
2026 Quantum Chemical Topology Analysis of Covalent Interactions in the Hydration of F- along with the Zinc Finger of NPL4 and Its Application to the Delimitation of QM/MM Boundaries. ACS omega 0 41939387
2025 NPLOC4 constructs tumor immunosuppressive microenvironment in pan-cancer and hepatocellular carcinoma. Current medicinal chemistry 0 40685720

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