Affinage

NSMCE4A

Non-structural maintenance of chromosomes element 4 homolog A · UniProt Q9NXX6

Round 2 corrected
Length
385 aa
Mass
44.3 kDa
Annotated
2026-04-29
39 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NSMCE4A is the kleisin subunit of the SMC5/6 complex, essential for complex integrity, DNA repair, and transcriptional silencing of episomal DNA. It bridges the SMC5 and SMC6 ATPase heads and physically engages NSMCE3 (MAGEG1/NSE3) through a conserved hydrophobic interface; depletion of NSMCE4A or disruption of this interface destabilizes all other SMC5/6 subunits (PMID:18086888, PMID:27427983). The SMC5/6 complex containing NSMCE4A is recruited to double-strand breaks where it promotes cohesin loading and sister-chromatid homologous recombination, and in ALT cancer cells it directs telomere targeting to APBs to support telomeric HR (PMID:16810316, PMID:17589526). NSMCE4A has a paralog-specific, non-redundant role in gating the SMC5/6 ring around episomal DNA—the initial step of a three-stage transcriptional silencing pathway—and additionally links the complex to the COP9 signalosome through direct interaction with GPS1 (PMID:36097294, PMID:32384871).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2005 High

    Identification of yeast Nse4 as the kleisin subunit of the essential Smc5/6 complex resolved which protein bridges the SMC heads and showed that its loss triggers checkpoint-dependent cell-cycle arrest and genome instability.

    Evidence Temperature-sensitive mutant generation, two-hybrid mapping, and genetic suppression in S. cerevisiae

    PMID:15752197

    Open questions at the time
    • Human ortholog had not yet been characterized
    • No structural information on how Nse4 bridges the SMC heads
  2. 2006 High

    Demonstrating that the SMC5/6 complex is recruited to DSBs and specifically promotes sister-chromatid HR—but not other HR sub-pathways or NHEJ—established the pathway-level function of the NSMCE4A-containing complex in DNA repair.

    Evidence RNAi of SMC5/6 subunits combined with multiple HR reporter assays and ChIP at nuclease-induced DSBs in human cells

    PMID:16810316

    Open questions at the time
    • Mechanism by which SMC5/6 recruits cohesin to DSBs was undefined
    • Whether NSMCE4A has subunit-specific contributions beyond complex integrity was unknown
  3. 2007 High

    Characterization of the full human SMC5/6 complex showed that NSMCE4A stability is interdependent with all other non-SMC subunits and that the complex supports telomere maintenance in ALT cells via MMS21-mediated SUMOylation of TRF1/TRF2 and APB targeting.

    Evidence RNAi knockdown, reciprocal co-IP, MMS sensitivity assays in human cells; immunofluorescence, SUMO modification assays, and telomere length analysis in ALT cells

    PMID:17589526 PMID:18086888

    Open questions at the time
    • Whether NSMCE4A has functions separable from the assembled SMC5/6 complex was unresolved
    • Structural basis of the kleisin-SMC interaction was lacking
  4. 2011 High

    Mapping the conserved hydrophobic interface between NSMCE3 (Nse3/MAGEG1) and NSMCE4A, and showing this subcomplex co-activates SF1-dependent transcription, revealed both the assembly mechanism and an unexpected non-repair function.

    Evidence Site-directed mutagenesis, yeast two-hybrid, co-IP, and transcriptional reporter assays in mammalian cells

    PMID:21364888

    Open questions at the time
    • Physiological significance of SF1 transcriptional co-activation was not explored in vivo
    • Whether the transcriptional role is separable from the SMC5/6 complex context remained unclear
  5. 2015 Medium

    Discovery that NSMCE4A scaffolds a TRIM31–MAGEA1–NSE4 complex that stimulates TRIM31 ubiquitin-ligase activity revealed an SMC5/6-independent function for the kleisin as an adaptor linking MAGE proteins to E3 ligases.

    Evidence Yeast two-hybrid screen, co-IP, and in vitro ubiquitin-ligase activity assays

    PMID:25590999

    Open questions at the time
    • Substrates of the TRIM31–MAGEA1–NSE4 ubiquitin ligase are unknown
    • In vivo relevance and tissue context not established
    • Single-lab finding without independent replication
  6. 2016 Medium

    Human genetic evidence that biallelic NSMCE3 mutations disrupt NSMCE4A interaction and destabilize the entire SMC5/6 complex, causing chromosome rearrangements, demonstrated that complex integrity via the NSMCE4A–NSMCE3 interface is essential for genome maintenance in humans.

    Evidence Whole-exome sequencing of patients, co-IP of mutant proteins, and functional assays in patient-derived cells

    PMID:27427983

    Open questions at the time
    • NSMCE4A role inferred through complex disruption rather than direct NSMCE4A mutation
    • Whether partial complex disruption produces graded phenotypes was not tested
  7. 2020 Medium

    Identification of a direct NSMCE4A–GPS1 interaction linked the SMC5/6 complex to the COP9 signalosome and showed that CSN activity modulates SMC5/6 accumulation at DNA damage sites, revealing a regulatory input to SMC5/6 function.

    Evidence Yeast two-hybrid, co-IP, immunofluorescence co-localization, laser micro-irradiation, and pharmacological CSN inhibition

    PMID:32384871

    Open questions at the time
    • Molecular mechanism by which CSN deneddylase activity limits SMC5/6 at damage sites is undefined
    • Whether GPS1 interaction is constitutive or damage-induced was not resolved
    • Single-lab observation
  8. 2022 High

    Paralog-swap experiments established that NSMCE4A—but not its paralog NSMCE4B—is specifically required for the DNA-entrapment step that initiates episomal silencing, demonstrating a non-redundant, gate-specific function of this kleisin isoform.

    Evidence Functional complementation of Nse4a vs Nse4b, ATPase-dead mutants, and episomal silencing reporters in human cells

    PMID:36097294

    Open questions at the time
    • Structural determinants distinguishing NSMCE4A from NSMCE4B in gate opening are unknown
    • Whether NSMCE4A-specific entrapment extends to all episomal DNA or is context-dependent was not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the structural basis for NSMCE4A's paralog-specific DNA-entrapment activity, in vivo substrates of the TRIM31–MAGEA1–NSE4 E3 ligase, and whether the NSMCE4A–GPS1 axis represents a regulated switch controlling SMC5/6 chromatin association.
  • No high-resolution structure of human NSMCE4A within the SMC5/6 complex
  • NSMCE4A-specific residues required for DNA entrapment not mapped
  • Physiological relevance of NSMCE4A functions outside SMC5/6 not established

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 3 GO:0060090 molecular adaptor activity 3
Localization
GO:0005634 nucleus 5 GO:0005694 chromosome 2
Pathway
R-HSA-73894 DNA Repair 4 R-HSA-1640170 Cell Cycle 3 R-HSA-4839726 Chromatin organization 2
Partners
GPS1MAGEG1NSMCE1NSMCE3SMC5SMC6TRIM31
Complex memberships
SMC5/6 complexTRIM31-MAGEA1-NSE4 complex

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 Yeast Qri2 (renamed Nse4, the ortholog of NSMCE4A) was identified as a component of the essential Smc5/6 DNA repair complex in S. cerevisiae. Temperature-sensitive nse4 mutants arrest after S phase in a Rad24 checkpoint-dependent manner with Rad53 phosphorylation, display genome instability and DNA damage sensitivity. Two-hybrid screens showed Nse4 physically interacts with other non-SMC elements of Smc5/6, and overexpression of known Smc5/6 subunits suppresses nse4(ts) arrest, placing Nse4 as the kleisin subunit essential for complex function. Temperature-sensitive mutant generation, two-hybrid screen, genetic suppression assays, cell-cycle analysis Molecular microbiology High 15752197
2007 The human SMC5-6 complex was fully characterized and its non-SMC components identified, including hNSE4 (NSMCE4A) as the kleisin subunit. Depletion of any non-SMC subunit (except hMMS21/hNSE2) causes degradation of all other complex subunits, demonstrating that NSMCE4A stability is interdependent with the integrity of the entire complex. Depletion confers sensitivity to methyl methanesulfonate, and several subunits are modified by sumoylation and ubiquitination. RNAi knockdown, co-immunoprecipitation, Western blot, MMS sensitivity assays Molecular and cellular biology High 18086888
2006 The human SMC5/6 complex (containing NSMCE4A) is recruited to nuclease-induced DNA double-strand breaks and is required for the subsequent recruitment of cohesin to DSBs. RNAi knockdown of SMC5/6 specifically impairs sister chromatid homologous recombination (HR) but not NHEJ, intra-chromatid HR, homologue HR, or extrachromosomal HR, defining NSMCE4A's complex role in the sister-chromatid HR sub-pathway. RNAi knockdown, gene targeting assays, ChIP at nuclease-induced DSBs, HR reporter assays The EMBO journal High 16810316
2007 The SMC5/6 complex (containing NSMCE4A) localizes to APBs (ALT-associated PML bodies) in ALT cancer cells and is required for targeting telomeres to APBs. The MMS21 SUMO ligase within the complex SUMOylates telomere-binding proteins TRF1 and TRF2, and inhibition of this SUMOylation prevents APB formation. Depletion of SMC5/6 subunits inhibits telomere HR, causing telomere shortening and senescence in ALT cells. RNAi, immunofluorescence co-localization, co-immunoprecipitation, SUMO modification assays, telomere length analysis Nature structural & molecular biology High 17589526
2011 Conserved interactions between Nse3 (MAGEG1 in mammals) and Nse4 (NSMCE4A/NSE4b in mammals) were mapped: a hydrophobic surface on the C-terminal MAGE-homology domain of Nse3 mediates binding to Nse4, and these interactions are conserved in human MAGEG1–NSE4b. Additionally, interaction of MAGEG1 with NSE4b results in transcriptional co-activation of the nuclear receptor steroidogenic factor 1 (SF1), revealing a non-DNA-repair function for the Nse3-Nse4 subcomplex. Site-directed mutagenesis, yeast two-hybrid, co-immunoprecipitation, molecular modelling, transcriptional reporter assays PloS one High 21364888
2015 TRIM31 directly binds NSE4 (NSMCE4A) and forms a TRIM31-MAGEA1-NSE4 complex that is structurally reminiscent of the ancestral NSE1-NSE3-NSE4 trimer of the SMC5/6 complex. MAGEA1 interaction stimulates the ubiquitin-ligase activity of TRIM31, identifying NSE4 as a scaffold linking MAGE proteins to RING-finger E3 ligases outside the SMC5/6 complex context. Yeast two-hybrid screen, co-immunoprecipitation, ubiquitin-ligase activity assays Cell cycle (Georgetown, Tex.) Medium 25590999
2016 Biallelic missense mutations in NSMCE3 disrupt its interactions with other SMC5/6 subunits including NSMCE4A, leading to destabilization of the entire complex. Patient cells show chromosome rearrangements, micronuclei, replication stress sensitivity, and defective homologous recombination, demonstrating that complex integrity (requiring proper NSMCE4A–NSMCE3 interaction) is essential for genome maintenance in human cells. Whole exome sequencing, co-immunoprecipitation, patient cell functional assays (chromosome analysis, HR assays, DNA damage sensitivity) The Journal of clinical investigation Medium 27427983
2020 A yeast two-hybrid screen using NSMCE4A as bait discovered a direct interaction between NSMCE4A (kleisin subunit of SMC5/6) and GPS1, a component of the COP9 signalosome (CSN). This interaction was confirmed by co-immunoprecipitation. GPS1 and SMC5/6 components co-localize during interphase and mitosis. Depletion of GPS1 or pharmacological inhibition of CSN deneddylase activity both increased SMC5/6 levels at laser-induced DNA damage sites, linking the CSN complex to regulation of SMC5/6 at DNA damage foci. Yeast two-hybrid, co-immunoprecipitation, immunofluorescence co-localization, laser micro-irradiation, CSN inhibition BMC molecular and cell biology Medium 32384871
2022 Transcriptional silencing of episomal DNA by the human SMC5/6 complex is a three-step process. The first step — entrapment of episomal DNA — requires Smc5/6 ATPase activity and a specific function of Nse4a (NSMCE4A) that cannot be substituted by its paralog Nse4b. The second step involves recruitment to PML nuclear bodies via SLF2/Nse6. The third step requires Nse2 (but not its SUMO ligase activity) for silencing. Thus NSMCE4A has a non-redundant, paralog-specific role in the initial DNA-entrapment step of episomal silencing. Functional complementation assays (Nse4a vs Nse4b paralog swap), ATPase-dead mutants, episomal silencing reporter assays, PML body localization Nature structural & molecular biology High 36097294
2025 Tandem affinity purification coupled with mass spectrometry identified a novel interaction between TOP3A (topoisomerase III alpha) and NSMCE4A, suggesting a physical link between the SMC5/6 complex and the topoisomerase machinery for resolving topological stress. Tandem affinity purification mass spectrometry (AP-MS) under normal and stressed conditions Molecular & cellular proteomics : MCP Low 41043513

Source papers

Stage 0 corpus · 39 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2010 MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. Molecular cell 388 20864041
2007 The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins. Nature structural & molecular biology 312 17589526
2018 Mapping the Genetic Landscape of Human Cells. Cell 225 30033366
2006 Human SMC5/6 complex promotes sister chromatid homologous recombination by recruiting the SMC1/3 cohesin complex to double-strand breaks. The EMBO journal 224 16810316
2013 The protein interaction landscape of the human CMGC kinase group. Cell reports 174 23602568
2008 Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PloS one 148 18461144
2004 Large-scale cDNA transfection screening for genes related to cancer development and progression. Proceedings of the National Academy of Sciences of the United States of America 82 15498874
2020 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell reports 79 32814053
2007 Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex. Molecular and cellular biology 79 18086888
2016 Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. The Journal of clinical investigation 64 27427983
2004 The DNA sequence and comparative analysis of human chromosome 10. Nature 52 15164054
2022 NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nature immunology 46 36138187
2011 Interactions between the Nse3 and Nse4 components of the SMC5-6 complex identify evolutionarily conserved interactions between MAGE and EID Families. PloS one 46 21364888
2015 The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. Cell cycle (Georgetown, Tex.) 40 25590999
2014 The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Molecular & cellular proteomics : MCP 40 25277244
2013 The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition. The Journal of biological chemistry 40 24163370
2022 In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane-Permeable, and Alkynyl-Enrichable Crosslinker. Analytical chemistry 38 35575683
2005 Qri2/Nse4, a component of the essential Smc5/6 DNA repair complex. Molecular microbiology 38 15752197
2020 Mutual regulation between OGT and XIAP to control colon cancer cell growth and invasion. Cell death & disease 36 32994395
2019 The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development. The Plant cell 32 31036599
2022 Smc5/6 silences episomal transcription by a three-step function. Nature structural & molecular biology 28 36097294
2019 Ultrastructure and Dynamics of Synaptonemal Complex Components During Meiotic Pairing and Synapsis of Standard (A) and Accessory (B) Rye Chromosomes. Frontiers in plant science 20 31281324
2019 Arabidopsis NSE4 Proteins Act in Somatic Nuclei and Meiosis to Ensure Plant Viability and Fertility. Frontiers in plant science 20 31281325
2021 Induced pluripotent stem cells from subjects with Lesch-Nyhan disease. Scientific reports 15 33875724
2024 Developing diagnostic biomarkers for Alzheimer's disease based on histone lactylation-related gene. Heliyon 10 39315143
2020 Interaction between NSMCE4A and GPS1 links the SMC5/6 complex to the COP9 signalosome. BMC molecular and cell biology 7 32384871
2024 Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes. Genes 4 39336750
2025 Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions. Molecular & cellular proteomics : MCP 0 41043513