Affinage

UFD1

Ubiquitin recognition factor in ER-associated degradation protein 1 · UniProt Q92890

Length
307 aa
Mass
34.5 kDa
Annotated
2026-06-10
64 papers in source corpus 35 papers cited in narrative 37 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

UFD1 (UFD1L) is the obligate substrate-recruiting subunit of a ubiquitin-selective unfoldase/segregase that, together with NPL4, forms a heterodimeric adaptor for the AAA+ ATPase p97/VCP (Cdc48 in yeast) and directs its ATP-driven extraction of ubiquitinated proteins from membranes, chromatin, protein complexes, and ribosomes for proteasomal degradation (PMID:10811609, PMID:11733065, PMID:28512218). The Ufd1-Npl4 heterodimer engages p97 in a defined geometry — one elongated bilobed heterodimer bound at the periphery of the N-D1 plane of one p97 hexamer — via the Ufd1 SHP box, which docks through hydrophobic contacts onto the Nc lobe of the p97 N-terminal domain, while Npl4 contributes a β-grasp ubiquitin-like domain interface; this assembly is mutually exclusive with the alternative p97 cofactor p47 (PMID:10811609, PMID:17202270, PMID:17491009, PMID:27684549, PMID:36087575). Substrate selection is achieved by recognition of K48-linked polyubiquitin chains synergistically by p97 and a conserved N-terminal ubiquitin-binding site of Ufd1, with the Ufd1 UT3 domain binding the proximal-side ubiquitin to direct the initiator ubiquitin into Npl4 for unfolding and engagement by the Cdc48 ATPase (PMID:12847084, PMID:28512218, PMID:36736315). Beyond ubiquitin, a Ufd1 SUMO-interaction motif lets the complex act as a dual receptor for SUMO-ubiquitin hybrid (STUbL-target) chains, enhancing unfolding and supporting genome-stability functions (PMID:22730331, PMID:36574706). Through this segregase activity UFD1 executes ER-associated degradation of substrates including HMG-CoA reductase, IP3 receptors and tyrosinase, retrotranslocating polyubiquitinated proteins to the cytosol (PMID:12847084, PMID:16103111, PMID:17681147, PMID:27684549), and acts more broadly in cell-cycle and chromatin control — driving degradation of SCF-βTrCP targets IκBα and CDC25A, antagonizing Aurora B on mitotic chromosomes, and extracting the CMG replicative helicase and centromeric CENP-A from chromatin (PMID:21486945, PMID:24248593, PMID:24429874, PMID:28355556, PMID:38526189). Complex output is tuned by UBX cofactors (FAF1, FAF2, UBXN7, VCF1/FAM104A) that lower the ubiquitin threshold for substrate engagement (PMID:35920641, PMID:38503733), and by post-translational control — PKA phosphorylation of Ufd1 S229 weakens p97 binding and inhibits ERAD, while Trim21-mediated K27-linked ubiquitination blocks Ufd1 incorporation into the VCP complex (PMID:31477623, PMID:39368714).

Mechanistic history

Synthesis pass · year-by-year structured walk · 16 steps
  1. 2000 High

    Established that Ufd1-Npl4 is a discrete p97 cofactor module that competes with p47, defining p97 as a multifunctional ATPase whose pathway specificity is set by mutually exclusive adaptors.

    Evidence Co-IP and competitive binding with Golgi membrane-fusion functional assay in mammalian systems

    PMID:10811609

    Open questions at the time
    • Did not define the substrate range or molecular mechanism of extraction
    • Structural basis of competition with p47 not yet resolved
  2. 2002 High

    Showed the Cdc48(Ufd1/Npl4) complex is a ubiquitin-selective segregase that liberates ubiquitinated substrates from partners and is a constitutive ERAD component, linking the adaptor to a defined degradation pathway.

    Evidence Yeast genetics, ubiquitin-binding and nuclear-translocation assays (SPT23), cycloheximide-chase degradation (OLE1)

    PMID:11733065 PMID:11847109

    Open questions at the time
    • Did not reconstitute the extraction reaction in vitro
    • Did not map the ubiquitin-recognition determinants on Ufd1
  3. 2003 High

    Reconstituted ER retrotranslocation and identified a conserved N-terminal ubiquitin-binding site in Ufd1 that, together with p97 and ATP hydrolysis by D1/D2, recognizes K48 chains and extracts substrates — defining the core biochemical mechanism.

    Evidence In vitro retrotranslocation reconstitution with ATPase-domain and ubiquitin-binding mutants

    PMID:12847084

    Open questions at the time
    • Atomic structure of the ubiquitin-bound complex not yet available
    • How the chain is threaded/unfolded not resolved
  4. 2007 High

    Resolved the architecture and docking interfaces of the Ufd1-Npl4-p97 assembly, defining the Ufd1 SHP box and Npl4 UBL contacts with the p97 N domain and the 1:1 heterodimer-per-hexamer stoichiometry.

    Evidence EM, analytical ultracentrifugation, native MS, and NMR chemical-shift mapping of intact 400-kDa complex

    PMID:17202270 PMID:17491009

    Open questions at the time
    • Low-resolution EM left side-chain interactions undefined
    • Did not capture nucleotide-dependent conformational states
  5. 2007 High

    Connected Ufd1 to a specific ER E3 ligase by showing it is a gp78 cofactor whose mono- and poly-ubiquitin-binding sites act at distinct ERAD steps, separating substrate ubiquitination from post-ubiquitination handling.

    Evidence Co-IP, in vitro ubiquitination, domain mutagenesis and cycloheximide chase of HMG-CoA reductase

    PMID:17681147

    Open questions at the time
    • Generality across other ER ligases not tested
    • Structural basis of the gp78-Ufd1 interaction unresolved
  6. 2011 High

    Extended UFD1 function beyond ERAD into mitotic and cell-cycle control, showing it antagonizes Aurora B on chromosomes and stabilizes Skp2 via USP13 recruitment under ER stress.

    Evidence siRNA depletion with live imaging and pharmacological epistasis; Co-IP and ubiquitination/cell-cycle assays

    PMID:21486945 PMID:21571647

    Open questions at the time
    • Direct substrate of p97-Ufd1 on chromosomes not biochemically defined in the Aurora B work
    • USP13 recruitment mechanism single-lab
  7. 2012 Medium

    Defined a SUMO-interaction motif in Ufd1, establishing the complex as a dual SUMO/ubiquitin receptor for STUbL targets and linking it to genome-stability pathways.

    Evidence Pulldown, yeast two-hybrid, genetic epistasis and DNA-damage sensitivity assays

    PMID:22730331 PMID:24265825

    Open questions at the time
    • Structural detail of SUMO engagement not resolved at this stage
    • Mammalian relevance of SIM-dependent functions not demonstrated
  8. 2014 Medium

    Showed the complex acts downstream of SCF-βTrCP to degrade specific signaling substrates (IκBα, CDC25A), connecting p97-UFD1-NPL4 to NF-κB activation and the G2/M checkpoint.

    Evidence Co-IP, siRNA knockdown, NF-κB reporter and cell-cycle/checkpoint assays

    PMID:24248593 PMID:24429874

    Open questions at the time
    • Single-lab Co-IP without reciprocal structural validation
    • Direct extraction of these substrates not reconstituted
  9. 2016 High

    Provided atomic detail of the Ufd1 SHP box bound to the p97 N domain and showed its mutation blocks ERAD, cementing the docking interface as functionally essential.

    Evidence 1.55 Å crystal structure, ITC, Co-IP and cycloheximide-chase ERAD assay

    PMID:27684549

    Open questions at the time
    • Did not address how SHP-box binding couples to the catalytic cycle
  10. 2017 High

    Demonstrated chromatin/replication functions by showing Ufd1-Npl4 recruits Cdc48 to K29-ubiquitinated Mcm7 to disassemble the CMG helicase at replication termination, and reconstituted ATP- and ubiquitination-dependent unfolding in vitro.

    Evidence Yeast extract reconstitution with Mcm7 ubiquitin-site mutagenesis; in vitro Ub-GFP unfoldase and ATPase assays

    PMID:28355556 PMID:28512218

    Open questions at the time
    • Branched-chain stimulation mechanism not structurally defined
    • How CMG is selected versus other chromatin substrates unclear
  11. 2019 High

    Resolved K48-linkage selectivity and the unfolding initiation step structurally, showing Npl4 reads K48-diubiquitin and that MSP-associated p97 mutants tighten Ufd1-Npl4 binding and accelerate unfolding, implicating gain-of-function pathology.

    Evidence Crystal structures of Npl4-K48-diUb; cryo-EM and quantitative unfoldase/affinity assays of MSP mutants

    PMID:31623962 PMID:31836717

    Open questions at the time
    • MSP mutations are in p97, not UFD1; UFD1 disease role not established
    • Physiological consequence of faster unfolding not shown in vivo
  12. 2019 Medium

    Identified PKA phosphorylation of Ufd1 S229 in the SHP box as a negative regulator of ERAD acting by weakening p97 binding, providing a signal-responsive control point.

    Evidence In vitro kinase assay, phosphomimetic mutagenesis, Co-IP and ERAD substrate accumulation

    PMID:31477623

    Open questions at the time
    • Single-lab; physiological PKA stimulus not defined
    • In vivo phospho-occupancy not quantified
  13. 2022 High

    Defined how cofactors and chain architecture set the ubiquitin threshold: UBX proteins (UBXN7, FAF1, FAF2) stabilize productive UFD1-NPL4-ubiquitin engagement for chains ≥5, and SUMO on hybrid chains enhances unfolding via Ufd1-SUMO contacts.

    Evidence Reconstituted CMG-disassembly and unfoldase assays, gene knockouts, cryo-EM and competition assays

    PMID:35920641 PMID:36574706

    Open questions at the time
    • Hierarchy among UBX cofactors in vivo not fully resolved
    • Structural detail of SUMO engagement at the complex limited
  14. 2023 High

    Pinpointed the Ufd1 UT3 domain as the determinant that selects the initiator ubiquitin on the proximal side of K48 chains, explaining efficient processing of 4-6-ubiquitin chains and the inhibitory effect of distal ubiquitins.

    Evidence FRET kinetics, domain mutagenesis and reconstituted unfolding

    PMID:36736315

    Open questions at the time
    • How cofactors relieve distal-ubiquitin inhibition addressed only partially
    • In-cell validation of UT3 selectivity pending
  15. 2024 Medium

    Broadened the substrate landscape and regulation: UFD1 delivers DTX2-ubiquitinated FTO to the proteasome and extracts centromeric CENP-A, while Trim21 K27-ubiquitination and VCF1/FAM104A respectively inhibit and stimulate UFD1-NPL4 function.

    Evidence Co-IP, linkage-specific ubiquitination assays, ChIP/artificial recruitment, mouse models and proteasomal degradation assays

    PMID:38503733 PMID:38526189 PMID:39368714 PMID:39661064

    Open questions at the time
    • Each finding single-lab without orthogonal structural confirmation
    • Mechanism of Trim21/VCF1 modulation not structurally resolved
  16. 2025 High

    Refined the cofactor mechanism and extended it to ribosome quality control: Faf1 braces the Ufd1 UT3 domain for initiator-ubiquitin unfolding, and Cdc48-Ufd1-Npl4 is recruited via Ltn1/Rqc1 to extract stalled ubiquitinated peptides from the 60S ribosome.

    Evidence Reconstituted human unfoldase assays, FRET kinetics and cryo-EM (both preprints)

    Open questions at the time
    • Both studies are preprints awaiting peer review
    • RQC recruitment functional consequences only inferred

Open questions

Synthesis pass · forward-looking unresolved questions
  • How UFD1's distinct activities — ERAD, chromatin/replication extraction, RQC, and SUMO-directed genome stability — are coordinately regulated and prioritized within a cell, and whether UFD1 itself carries disease-causing variants, remains unresolved.
  • No timeline evidence links UFD1 mutations to a Mendelian disease
  • Cell-context rules governing substrate triage by a single shared adaptor are undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 6 GO:0098772 molecular function regulator activity 4 GO:0140313 molecular sequestering activity 3
Localization
GO:0005783 endoplasmic reticulum 5 GO:0005634 nucleus 4 GO:0005694 chromosome 3 GO:0005829 cytosol 2
Pathway
R-HSA-392499 Metabolism of proteins 5 R-HSA-1640170 Cell Cycle 3 R-HSA-69306 DNA Replication 2 R-HSA-8953897 Cellular responses to stimuli 2 R-HSA-8953854 Metabolism of RNA 1
Partners
FAF1FAF2GP78NPL4TRIM21UBXN7USP13VCP
Complex memberships
ERAD machineryp97-Ufd1-Npl4 (Cdc48-Ufd1-Npl4) segregase

Evidence

Reading pass · 37 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 Mammalian Ufd1 and Npl4 form a binary heterodimer that binds p97/VCP; Ufd1-Npl4 competes with p47 for binding to the p97 N-terminal domain, making the two complexes mutually exclusive and directing p97 to distinct cellular pathways. Co-immunoprecipitation, competitive binding assays, Golgi membrane fusion inhibition assay The EMBO journal High 10811609
2001 The CDC48(UFD1/NPL4) complex acts as a ubiquitin-selective chaperone/segregase that liberates ubiquitinated, processed SPT23 transcription factor from its membrane-tethered unprocessed partner, enabling nuclear targeting; the complex binds preferentially to ubiquitinated substrates. Yeast genetics, co-immunoprecipitation, in vivo ubiquitin binding assay, nuclear translocation assay Cell High 11733065
2002 CDC48(UFD1/NPL4) is a constitutive component of the ERAD machinery in yeast, required for degradation of OLE1 and other ERAD substrates; it acts as a segregase liberating ubiquitylated proteins from non-modified partners prior to proteasomal degradation. Yeast genetics, cycloheximide chase degradation assays, epistasis analysis The EMBO journal High 11847109
2003 The p97-Ufd1-Npl4 complex mediates retrotranslocation of polyubiquitinated substrates from the ER membrane to the cytosol. Polyubiquitin chains (K48-linked) are recognized synergistically by both p97 and an evolutionarily conserved ubiquitin-binding site at the N-terminus of Ufd1. The D1 domain of p97 in its nucleotide-bound state is required for substrate binding, and alternating ATP hydrolysis by D1 and D2 drives polypeptide extraction. In vitro retrotranslocation reconstitution, ATPase domain mutant analysis, ubiquitin-binding domain mapping, ER membrane binding assays The Journal of cell biology High 12847084
2005 The p97-Ufd1-Npl4 complex associates with ubiquitinated IP3 receptors upon hormonal stimulation and is required for their ERAD; p97 knockdown by RNAi markedly retards hormone-induced IP3 receptor degradation and increases accumulation of ubiquitinated IP3 receptors. Co-immunoprecipitation, RNAi knockdown, pulse-chase degradation assays in mammalian cells 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, a stoichiometry and arrangement distinct from the p97-p47 complex. Electron microscopy, analytical ultracentrifugation, native mass spectrometry Proceedings of the National Academy of Sciences of the United States of America High 17202270
2007 Ufd1 binds p97 via its SHP box region interacting with the Nc lobe of the p97 N-terminal domain; the Npl4 ubiquitin-like domain (UBD) adopts a β-grasp fold and binds a defined surface of the p97 N domain; NMR chemical shift perturbation mapping confirmed an identical interaction mode in the full 400-kDa p97-UN complex. NMR solution structure, chemical shift perturbation analysis, backbone amide assignment of p97 N domain The Journal of biological chemistry High 17491009
2007 Ufd1 directly interacts with the ER ubiquitin ligase gp78 and functions as its cofactor, enhancing gp78 E3 activity and accelerating ubiquitination and degradation of HMG-CoA reductase. The monoubiquitin-binding site of Ufd1 is required for enhancement of gp78 activity, whereas the polyubiquitin-binding site is critical for a post-ubiquitination ERAD step. Co-immunoprecipitation, in vitro ubiquitination assay, domain mutagenesis, cycloheximide chase Cell metabolism High 17681147
2010 In US2-expressing cells, p97 dislocates MHC class I heavy chain from the ER independently of Ufd1-Npl4, demonstrating that p97 can employ Ufd1-Npl4-independent mechanisms for ERAD retrotranslocation depending on the substrate/viral hijacking context. In vitro permeabilized-cell retrotranslocation assay, immunodepletion of Ufd1-Npl4 The Journal of biological chemistry Medium 20702414
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 and multi-lobed nuclei. Low-dose Aurora B inhibitor partially rescues chromosome alignment in Ufd1-depleted cells. siRNA knockdown, live-cell imaging, immunofluorescence, pharmacological epistasis (hesperadin) Journal of cell science High 21486945
2011 Nuclear Ufd1 recruits the deubiquitinating enzyme USP13 to counteract APC/C(Cdh1)-mediated ubiquitination of Skp2; downregulation of Ufd1 during prolonged ER stress enhances Skp2 ubiquitination/destabilization, causing p27 accumulation and G1 cell cycle delay. Co-immunoprecipitation, siRNA knockdown, ubiquitination assay, cell cycle analysis, Western blot Proceedings of the National Academy of Sciences of the United States of America Medium 21571647
2012 Cryo-EM reconstructions show that Ufd1-Npl4 is highly dynamic relative to the p97 ring and assumes distinct positions upon nucleotide addition, suggesting that cofactor repositioning is coupled to the p97 ATPase cycle and substrate remodeling. Electron cryo-microscopy (cryo-EM) 3D reconstruction Proceedings of the National Academy of Sciences of the United States of America Medium 22232657
2012 Ufd1 contains a SUMO interaction motif (SIM) that enables Cdc48-Ufd1-Npl4 to bind SUMO directly, allowing the complex to act as a dual receptor for STUbL targets bearing both SUMO and ubiquitin modifications, with cooperative binding for genome stability functions. Pulldown assays, yeast two-hybrid, genetic epistasis, DNA damage sensitivity assays The Journal of biological chemistry Medium 22730331
2013 FAF1 interacts exclusively with VCP complexed with Npl4-Ufd1 heterodimer (not free VCP); VCP association to FAF1's UBX domain allosterically regulates ubiquitin binding to FAF1's UBA domain; the trimeric FAF1-VCP-Npl4-Ufd1 assembly promotes ERAD. Co-immunoprecipitation, structural analysis, biochemical domain interaction mapping The Journal of biological chemistry Medium 23293021
2013 The p97-UFD1L-NPL4 complex binds ubiquitinated IκBα via UFD1L's polyubiquitin-binding domain and via p97's interaction with SCF(β-TRCP); this complex facilitates IκBα proteasomal degradation after TNF-α or IL-1β stimulation, enabling NF-κB activation. Co-immunoprecipitation, siRNA knockdown, NF-κB reporter assay, Western blot Molecular and cellular biology Medium 24248593
2013 In fission yeast, Ufd1 physically interacts with the STUbL Rfp1 and SUMO E3 ligase Pli1 through its C-terminal domain; deletion of this domain causes accumulation of high-molecular-weight SUMO conjugates, genomic instability, and failure of homologous recombination repair; Ufd1 localizes to nuclear foci colocalizing with SUMO during the DNA damage response. Yeast two-hybrid, Co-IP, genetic epistasis, immunofluorescence localization, genotoxin sensitivity assays PloS one Medium 24265825
2014 p97-Ufd1-Npl4 binds CDC25A downstream of SCF-βTrCP ubiquitination and facilitates its proteasomal degradation during the G2/M DNA damage checkpoint; depletion of Ufd1-Npl4 causes G2/M checkpoint failure due to persistent CDC25A activity. Co-immunoprecipitation, siRNA knockdown, cell cycle analysis, Western blot Cell cycle (Georgetown, Tex.) Medium 24429874
2016 Crystal structure (1.55 Å) of the p97 N-terminal domain bound to the Ufd1 SHP box reveals that 11 residues of the SHP box (including F225, F228, N233, L235) bind the Nc lobe of p97 primarily through hydrophobic interactions; mutagenesis of these residues abolishes interaction and causes accumulation of the ERAD substrate tyrosinase-C89R. X-ray crystallography, isothermal titration calorimetry, co-immunoprecipitation, cycloheximide chase ERAD assay PloS one High 27684549
2017 Wild-type p97-NPLOC4-UFD1L unfolds ubiquitinated substrates in vitro in an ATP hydrolysis-dependent and substrate-ubiquitination-dependent manner; K48-linked branched ubiquitin chains provide maximal stimulation. A p97 MSP disease mutant unfolds substrates faster, suggesting gain-of-function pathogenesis. In vitro unfoldase assay with Ub-GFP substrate, ATPase assay, mutant p97 biochemical analysis 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 (specifically via K29-ubiquitinated Mcm7) at the end of chromosome replication to drive CMG disassembly; mutation of Mcm7 K29 abrogates Ufd1-Npl4-Cdc48 recruitment. Yeast cell extract reconstitution, Co-IP, mutagenesis of ubiquitylation sites, mass spectrometry Cell reports High 28355556
2017 Cdc48-Ufd1 is required for Dsc E3 ligase Golgi localization, a step upstream of Rbd2-mediated SREBP cleavage, in fission yeast; Cdc48-Ufd1 does not interact with the Cdc48-Rbd2 complex, demonstrating two distinct Cdc48 complexes act sequentially in SREBP activation. Affinity chromatography, mass spectrometry, genetic analysis, SREBP cleavage assay The Journal of biological chemistry Medium 28821619
2019 Crystal structures of yeast Npl4 bound to K48-linked diubiquitin reveal that the Npl4 C-terminal domain (CTD) N-terminal loop contacts proximal ubiquitin and C-terminal helix contacts distal ubiquitin, conferring K48-linkage selectivity; Ufd1 occupies a hydrophobic groove of the Npl4 MPN domain corresponding to the catalytic groove of JAMM-family DUBs. X-ray crystallography, mutational analysis Nature communications High 31836717
2019 All seven analyzed MSP p97 mutants exhibit tighter Ufd1-Npl4 (UN) binding and faster substrate unfolding than wild-type p97; cryo-EM structures suggest that increased UN affinity in MSP mutants originates from decoupling of p97 nucleotide state from N-terminal domain positioning. Cryo-EM, biochemical unfoldase assay, binding affinity measurements Structure (London, England : 1993) High 31623962
2019 Phosphorylation of Ufd1 at serine 229 (within the SHP box) by PKA negatively regulates ERAD by reducing Ufd1 binding affinity for VCP; a phosphomimetic S229D mutant inhibits ERAD and causes accumulation of ERAD substrates (tyrosinase-C89R, HMG-CoA reductase). In vitro kinase assay, phosphomimetic/non-phosphorylatable mutagenesis, co-immunoprecipitation, ERAD substrate accumulation assay The Biochemical journal Medium 31477623
2022 SUMO modification on substrates bearing SUMO-polyubiquitin hybrid chains enhances unfolding by Ufd1/Npl4/Cdc48 compared to polyubiquitin alone; cryo-EM structures reveal interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during ubiquitin unfolding, with Ufd1-SUMO interactions driving the preference. In vitro unfoldase assay, cryo-EM single-particle analysis, competition assay Proceedings of the National Academy of Sciences of the United States of America High 36574706
2022 Multiple UBX proteins (UBXN7, FAF1, FAF2) reduce the ubiquitin threshold of mammalian p97-UFD1-NPL4 for substrate unfolding by stabilizing productive UFD1-NPL4 interactions with K48-linked ubiquitin chains of ≥5 ubiquitins; FAF1/FAF2 act via a coiled-coil domain; deletion of Ubxn7 and Faf1 impairs CMG disassembly in S-phase and mitosis. Reconstituted CMG disassembly assay, gene knockout, biochemical ubiquitin threshold assay eLife High 35920641
2022 Crystal structures of the human Ufd1-Npl4 (UN) heterodimer at 2.7 Å reveal the atomic details of hUfd1-hNpl4 interaction; site-directed mutagenesis of hUfd1 residues confirmed the interface, showing conservation with but distinct features from yeast UN. X-ray crystallography, site-directed mutagenesis Structure (London, England : 1993) High 36087575
2023 Ufd1's UT3 domain binds a K48-linked ubiquitin on the proximal side of the initiator ubiquitin in a polyubiquitin chain, directing the initiator toward rapid unfolding by Npl4 and engagement by Cdc48; ubiquitins on the distal side increase substrate affinity but impede substrate release from Cdc48-Ufd1/Npl4 without additional cofactors; this mechanism explains efficient processing of K48-linked chains of 4-6 ubiquitins. FRET-based kinetic assays, domain mutagenesis, in vitro unfolding reconstitution Molecular cell High 36736315
2023 The Cdc48 N-terminal domain (NTD) stabilizes Ufd1-Npl4 (UN) assembly upon binding; a highly conserved cysteine C115 at the Cdc48-Npl4 interface is central to complex stability; C115S mutation disrupts Cdc48-NTD interaction with Npl4-Ufd1 and causes moderate decrease in yeast growth and protein quality control. Integrative structural modeling, crosslinking mass spectrometry, site-directed mutagenesis, yeast growth assay Structure (London, England : 1993) Medium 37311459
2024 FTO is ubiquitinated by its E3 ligase DTX2, followed by UFD1 recruitment and subsequent proteasomal degradation; UFD1 functions downstream of DTX2-mediated ubiquitination to deliver FTO to the proteasome. Co-immunoprecipitation, ubiquitination assay, genetic knockdown, in vivo mouse models Proceedings of the National Academy of Sciences of the United States of America Medium 39661064
2024 Trim21 E3 ligase interacts with UFD1 and catalyzes K27-linked ubiquitination of UFD1, inhibiting UFD1 incorporation into the VCP complex, thereby suppressing ERAD substrate degradation and activating a proapoptotic UPR. Co-immunoprecipitation, ubiquitination assay with linkage-specific detection, ERAD substrate accumulation assay, UPR reporter Biochimica et biophysica acta. Molecular basis of disease Medium 39368714
2024 VCF1 (FAM104A) co-purifies with p97-UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates; VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via high-affinity binding to the p97 N-domain but has no intrinsic ubiquitin affinity itself. Co-immunoprecipitation, pulldown, ubiquitin-binding assays, proteasomal degradation assay in cells Nature communications Medium 38503733
2024 Cdc48 together with its cofactor Ufd1 physically interacts with centromeric chromatin and, when artificially recruited to a mini-chromosome centromere, extracts CENP-A (Cnp1) from centromeric chromatin, causing increased chromosome loss; ufd1-73 mutant allows CENP-A mislocalization and increased centromeric CENP-A levels. Chromatin immunoprecipitation, artificial recruitment assay, yeast genetics, chromosome loss assay Biology open Medium 38526189
2020 UFD1 (but not NPL4) is required for EVA71 viral entry into host cells; UFD1 knockdown reduces binding and entry of EVA71 by modulating nucleolin protein levels, a co-receptor for EVA71, without affecting viral replication in replicon assays. siRNA knockdown, pseudovirus entry assay, replicon RNA transfection, Western blot for nucleolin Virus research Medium 32289342
1997 Yeast Ufd1 interacts with poly(A) polymerase (Pap1) and with Uba2; depletion of Ufd1 yields cell extracts defective in mRNA 3'-end processing/polyadenylation, though Ufd1 is not a component of canonical polyadenylation factors. Two-hybrid system, co-immunoprecipitation from yeast extracts, in vitro polyadenylation assay Molecular & general genetics : MGG Low 9236779
2025 Faf1 accelerates p97-UFD1-NPL4-dependent substrate unfolding by stabilizing productive ubiquitin engagement; its C-terminal UBX domain, while bound to p97, positions a long helix that braces the UT3 domain of Ufd1, stabilizing the Ufd1-Npl4 cofactor for initiator ubiquitin unfolding and engagement by the ATPase. Reconstituted in vitro unfoldase assay with human components, FRET-based assays, cryo-EM structure determination bioRxivpreprint High
2025 Cryo-EM structure of the yeast RQC complex shows that Cdc48 with its Ufd1-Npl4 adaptor is recruited by the Ltn1 E3 ubiquitin ligase to extract ubiquitylated stalled peptides from the 60S ribosome; Rqc1 bridges the 60S ribosome with ubiquitin and Ltn1, facilitating K48-linked polyubiquitin chain formation on stalled peptides as the signal for Cdc48-Ufd1-Npl4 recruitment. Cryo-EM structure determination, reconstituted RQC assay bioRxivpreprint Medium

Source papers

Stage 0 corpus · 64 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
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
2002 Cdc48-Ufd1-Npl4: stuck in the middle with Ub. Current biology : CB 132 12015140
2007 Structural insights into the p97-Ufd1-Npl4 complex. Proceedings of the National Academy of Sciences of the United States of America 81 17202270
2007 Ufd1 is a cofactor of gp78 and plays a key role in cholesterol metabolism by regulating the stability of HMG-CoA reductase. Cell metabolism 81 17681147
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
1997 UFD1L, a developmentally expressed ubiquitination gene, is deleted in CATCH 22 syndrome. Human molecular genetics 72 9063746
2011 Ubiquitin-recognition protein Ufd1 couples the endoplasmic reticulum (ER) stress response to cell cycle control. Proceedings of the National Academy of Sciences of the United States of America 71 21571647
2019 Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Structure (London, England : 1993) 58 31623962
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
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
2015 Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nature communications 36 26365526
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
2023 The Ufd1 cofactor determines the linkage specificity of polyubiquitin chain engagement by the AAA+ ATPase Cdc48. Molecular cell 30 36736315
2020 PCBP2 Posttranscriptional Modifications Induce Breast Cancer Progression via Upregulation of UFD1 and NT5E. Molecular cancer research : MCR 30 33037085
2001 Association study of a promoter polymorphism of UFD1L gene with schizophrenia. American journal of medical genetics 29 11496370
2018 UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. Leukemia 28 29743725
2016 Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation. PloS one 27 27684549
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
1997 The Uba2 and Ufd1 proteins of Saccharomyces cerevisiae interact with poly(A) polymerase and affect the polyadenylation activity of cell extracts. Molecular & general genetics : MGG 27 9236779
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
1998 Structure and expression of the human ubiquitin fusion-degradation gene (UFD1L). Biochimica et biophysica acta 22 9540831
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
2003 Functional attenuation of UFD1l, a 22q11.2 deletion syndrome candidate gene, leads to cardiac outflow septation defects in chicken embryos. Pediatric research 18 12612215
2013 Concerted action of the ubiquitin-fusion degradation protein 1 (Ufd1) and Sumo-targeted ubiquitin ligases (STUbLs) in the DNA-damage response. PloS one 16 24265825
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
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
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
1999 UFD1L and CDC45L: a role in DiGeorge syndrome and related phenotypes? Trends in genetics : TIG 11 10390621
2020 Involvement of VCP/UFD1/Nucleolin in the viral entry of Enterovirus A species. Virus research 10 32289342
2024 Targeting DTX2/UFD1-mediated FTO degradation to regulate antitumor immunity. Proceedings of the National Academy of Sciences of the United States of America 9 39661064
2022 Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Structure (London, England : 1993) 8 36087575
2001 A common cis-acting sequence in the DiGeorge critical region regulates bi-directional transcription of UFD1L and CDC45L. Mechanisms of development 8 11578863
2017 Dsc E3 ligase localization to the Golgi requires the ATPase Cdc48 and cofactor Ufd1 for activation of sterol regulatory element-binding protein in fission yeast. The Journal of biological chemistry 7 28821619
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
2011 RNA interference (RNAi) of Ufd1 protein can sensitize a hydroxycamptothecin-resistant colon cancer cell line SW1116/HCPT to hydroxycamptothecin. Journal of digestive diseases 6 21401896
2001 Characterization of the bi-directional transcriptional control region between the human UFD1L and CDC45L genes. Biochemical and biophysical research communications 6 11341762
2025 A UFD1 variant encoding a microprotein modulates UFD1f and IPMK ubiquitination to play pivotal roles in anti-stress responses. Nature communications 5 40691175
2013 Polymorphisms in schizophrenia candidate gene UFD1L may contribute to cognitive deficits. Psychiatry research 5 23623450
2008 A family- and population-based study of the UFD1L gene for schizophrenia. American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 5 18270977
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
2002 Functional characterization of the 5' flanking region of human ubiquitin fusion degradation 1 like gene (UFD1L). Cell biochemistry and function 4 11979512
2023 The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation. Structure (London, England : 1993) 3 37311459
2019 Ufd1 phosphorylation at serine 229 negatively regulates endoplasmic reticulum-associated degradation by inhibiting the interaction of Ufd1 with VCP. The Biochemical journal 3 31477623
2001 Cloning and molecular characterization of three ubiquitin fusion degradation 1 (Ufd1) ortholog genes from Xenopus laevis, Gallus gallus and Drosophila melanogaster. Cytogenetics and cell genetics 3 11435701
2024 Cdc48 and its co-factor Ufd1 extract CENP-A from centromeric chromatin and can induce chromosome elimination in the fission yeast Schizosaccharomyces pombe. Biology open 2 38526189
2003 Analysis of intracellular distribution and apoptosis involvement of the Ufd1l gene product by over-expression studies. Cell biochemistry and function 2 12910480

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