Affinage

INTS3

Integrator complex subunit 3 · UniProt Q68E01

Length
1043 aa
Mass
118.1 kDa
Annotated
2026-06-10
26 papers in source corpus 19 papers cited in narrative 19 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/7 claims corpus-supported (86%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

INTS3 is a dual-function scaffold protein that links single-stranded nucleic acid recognition to genome stability and RNA Polymerase II transcription regulation (PMID:19683501, PMID:25675981). As the central adaptor of the heterotrimeric SOSS1 complex (with hSSB1/2 and C9ORF80/INIP), INTS3 is required for assembly and stability of its partners and for accumulation of the complex at DNA ends, such that its loss confers ionizing-radiation sensitivity, defective G2/M checkpoint, chromosomal instability, and impaired homologous recombination (PMID:19683501, PMID:19605351). Domain dissection shows a bipartite architecture: the N-terminus mediates protein-protein interactions while the HEAT-repeat C-terminal domain forms a stable dimer that binds ssRNA/ssDNA (with higher affinity for ssRNA and a ~30-nt minimum, excluding duplexes and hybrids) and simultaneously docks INTS6 on a separate conserved surface; dimerization and the INTS3c/INTS6c interface are both required for efficient ssDNA recognition and double-strand break repair (PMID:29150435, PMID:33434574, PMID:34400606). Through these activities INTS3 promotes ATM/ATR-ATRIP checkpoint signaling, Chk1 phosphorylation, and the recruitment of RAD51 and BRCA1 to damage sites (PMID:19786574, PMID:23986477, PMID:25916848). At breaks, the SOSS1 complex engages transcription-associated structures, binding R-loops and tyrosine-1-phosphorylated RNAPII to nucleate liquid-like repair compartments, and recruits the MRN complex via a phospho-dependent Nbs1-FHA interaction (PMID:38039132, PMID:37705456). INTS3 is also an integral subunit of the Integrator complex, where it regulates snRNA processing, replication-dependent histone mRNA 3'-end processing, and promoter-proximal Pol II pausing in a DSIF-dependent manner (PMID:25675981); cryo-EM of the Integrator-PP2A complex places INTS3 in a post-termination position that blocks Pol II rebinding after termination (PMID:38570683). Consistent with an RNA-regulatory role, INTS3 destabilizes pro-apoptotic transcripts to support colorectal cancer cell survival (PMID:38665208).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2009 High

    Established INTS3 as the organizing scaffold of a DNA-damage-response complex, answering how single-stranded DNA-binding factors are stabilized and delivered to DNA ends.

    Evidence Reciprocal Co-IP, tandem affinity purification, and siRNA depletion with IR-sensitivity, checkpoint, and HR readouts in human cells

    PMID:19605351 PMID:19683501 PMID:19786574

    Open questions at the time
    • Did not define the structural basis of scaffolding
    • Direct nucleic-acid binding by INTS3 itself not yet shown
    • Relationship to Integrator transcription functions unaddressed
  2. 2013 High

    Identified INTS6 as a direct INTS3 partner that co-relocates to damage sites, extending the complex and linking it to RAD51/BRCA1 accumulation and HR.

    Evidence Affinity purification, in vitro binding, immunofluorescence foci, and HR assays; mouse conditional KO confirming SSB1 localization depends on INTS3

    PMID:23459151 PMID:23986477

    Open questions at the time
    • INTS6-INTS3 binding interface not structurally defined
    • Mechanism of RAD51/BRCA1 recruitment downstream unresolved
  3. 2015 High

    Placed INTS3 within the Integrator complex on RNA Pol II and showed it functions in checkpoint signaling when RPA is limiting, connecting transcription machinery to DNA-damage response.

    Evidence Affinity purification with HIT-Seq and RNA-processing depletion assays; siRNA epistasis with ATR-ATRIP foci and Chk1 phosphorylation readouts; nuclear-matrix proteomics

    PMID:25609707 PMID:25675981 PMID:25916848

    Open questions at the time
    • How INTS3 partitions between SOSS1 and Integrator roles unclear
    • Direct vs indirect role in snRNA/histone processing not separated for INTS3 specifically
  4. 2018 High

    Mapped INTS3 nucleic-acid binding to its C-terminus and protein interactions to its N-terminus, and showed it tunes hNABP1/2 binding, defining a bipartite functional architecture.

    Evidence EMSA, GST pulldown, and reconstitution with recombinant proteins; NMR showing hSSB1 tetramers retain INTS3 binding

    PMID:28609781 PMID:29150435

    Open questions at the time
    • Atomic structure of binding domains not yet determined
    • Physiological significance of ssRNA preference unresolved
  5. 2021 High

    Crystal structures defined the HEAT-repeat C-terminal domain as a dimer that binds ssDNA/ssRNA and INTS6 via distinct surfaces, with both dimerization and the INTS6 interface required for DSB repair.

    Evidence X-ray crystallography of INTS3c and INTS3c-INTS6c, mutagenesis, EMSA, protein-stability assays, and DSB repair functional assays

    PMID:33434574 PMID:34400606

    Open questions at the time
    • Structure of full-length INTS3 with hSSB1/C9ORF80 not solved
    • How dimerization couples to in vivo end resection unclear
  6. 2023 Medium

    Connected SOSS1 to transcription-coupled repair, showing it binds R-loops and Y1P RNAPII to form phase-separated repair compartments and recruits MRN via a phospho-Nbs1 interaction.

    Evidence Co-IP, in vitro binding, live-cell phase-separation imaging, siRNA repair assays; phosphopeptide binding with site-specific INTS3 mutants

    PMID:37705456 PMID:38039132

    Open questions at the time
    • In vivo requirement of phase separation for repair not genetically isolated
    • Kinase responsible for INTS3 T592 phosphorylation not identified
  7. 2024 High

    Cryo-EM resolved INTS3 within the Integrator-PP2A complex in a post-termination position that prevents Pol II rebinding, and INTS6 was shown to extend SOSS1 to a tetramer coupling PP2A/SETX to R-loop resolution.

    Evidence Cryo-EM of Integrator-PP2A in multiple functional states; Co-IP and functional assays of tetrameric SOSS1 with RNAPII dephosphorylation and SETX recruitment readouts

    PMID:38570683 PMID:39445827

    Open questions at the time
    • Structural state of INTS3 during active termination vs post-termination transition partly inferred
    • How the same INTS3 surface is shared between Integrator and SOSS1 roles in vivo unresolved
  8. 2024 Medium

    Defined an RNA-regulatory, anti-apoptotic role for INTS3 in cancer, destabilizing pro-apoptotic transcripts to sustain colorectal tumor cell survival.

    Evidence CRISPR-Cas9 screen, siRNA/RNA-seq, and in vivo tumor-growth assays with nanoparticle knockdown

    PMID:38665208

    Open questions at the time
    • Direct transcript targets and binding sites not mapped
    • Whether this depends on Integrator or SOSS1 context unknown
  9. 2022 Medium

    Linked INTS3 chromatin occupancy to PARP1 and SPT6, indicating its genomic recruitment is directed by transcription-associated factors.

    Evidence Co-IP, ChIP-seq, and siRNA knockdown for PARP1; ChIP-based loss-of-recruitment for SPT6 at U2 snRNA genes

    PMID:35625631 PMID:36291070

    Open questions at the time
    • SPT6 dependency rests on a single ChIP observation
    • Functional consequence of PARP1-directed INTS3 occupancy not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How INTS3 is partitioned between its SOSS1 DNA-repair role and its Integrator transcription-termination role, and whether the two functions are competitive or coordinated, remains unresolved.
  • No structure of full-length INTS3 simultaneously engaging both complexes
  • Regulatory switch governing complex choice unknown
  • Quantitative cellular distribution between the two roles unmeasured

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0005198 structural molecule activity 3 GO:0060090 molecular adaptor activity 3 GO:0003723 RNA binding 2
Localization
GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2
Pathway
R-HSA-73894 DNA Repair 3 R-HSA-74160 Gene expression (Transcription) 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-1640170 Cell Cycle 1
Partners
BAZ1BC9ORF80INTS6NBNPARP1RNAPIIRUNX2SSB1
Complex memberships
Integrator complexIntegrator-PP2A complexSOSS1 complex

Evidence

Reading pass · 19 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 INTS3 (SOSS-A) serves as a central adaptor/scaffold protein required for assembly and stability of the heterotrimeric SOSS complex (consisting of hSSB1/2, INTS3, and C9orf80/SOSS-C), and is required for facilitating the accumulation of the SOSS complex to DNA ends. SOSS-depleted cells display increased ionizing radiation sensitivity, defective G2/M checkpoint, and impaired homologous recombination repair. Co-immunoprecipitation, tandem affinity purification, siRNA depletion with functional readouts (IR sensitivity, checkpoint assays, HR assays) Molecular cell High 19683501
2009 INTS3 forms separate but structurally similar complexes with hSSB1 and hSSB2, each also containing hSSBIP1 (C9ORF80). Depletion of INTS3 decreases the stability of hSSB1 and hSSBIP1, indicating INTS3 provides a scaffold for proper assembly. Cells depleted of INTS3 exhibit hypersensitivity to DNA-damaging reagents, chromosomal instability, and reduced ATM-dependent phosphorylation. Co-immunoprecipitation, siRNA depletion, cellular assays (survival, chromosomal instability, ATM signaling) The Journal of biological chemistry High 19605351
2009 INTS3 copurifies with a subset of Integrator complex subunits and C9orf80/MISE when pulled down with hSSB1. The INTS3-MISE-hSSB1 complex plays a key role in ATM activation and RAD51 recruitment to DNA damage foci. INTS3 controls hSSB1 transcription, demonstrating a regulatory network for hSSB1 function. Tandem affinity purification of hSSB1 mutants (phosphomimetic and non-phosphorylatable), mass spectrometry, functional assays (ATM activation, RAD51 foci) The Journal of cell biology High 19786574
2013 INTS6 is a major subunit of the core hSSB1 complex, forming a stable complex with INTS3 and hSSB1 both in vitro and in vivo. INTS6 directly interacts with INTS3. In response to DNA damage, INTS6 relocates along with INTS3 and hSSB1 to DNA damage sites. The hSSB1-INTS complex regulates the accumulation of RAD51 and BRCA1 at DNA damage sites and the corresponding homologous recombination. Protein affinity purification, co-immunoprecipitation, in vitro binding assay, immunofluorescence (foci formation), HR assay Journal of cell science High 23986477
2013 mSSB1's interaction with INTS3 is required for its localization to damaged DNA, established in a mouse conditional knockout model. mSSB1 and mSSB2 localize to telomeres and are required to protect newly replicated telomeric G-overhangs. Conditional knockout mice, immunofluorescence, telomere dysfunction assays, co-immunoprecipitation Cell research Medium 23459151
2015 Complexes containing INTS3 and either NABP1 or NABP2 are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator (including INTS3-containing complexes) binds to 3' ends of replication-dependent histones and promoter-proximal regions of polyadenylated-transcript genes; depletion of Integrator subunits causes transcription termination failure, disruption of histone mRNA processing, and polyadenylation of snRNAs and histone mRNAs. Integrator recruitment to all three gene classes is DSIF-dependent. Affinity purification, HIV Integration targeting-sequencing (HIT-Seq), subunit depletion with RNA processing readouts Cell research High 25675981
2015 INTS3 interacts with RUNX2 and BAZ1B as part of subnuclear, nuclear-matrix-associated complexes in cancer cells. RUNX2, INTS3, and BAZ1B form UV-responsive complexes with γH2AX (phospho-H2AX Ser139) following DNA damage. Subnuclear foci containing INTS3 change in intensity or number following UV irradiation. Proteomic analysis (nuclear matrix pulldown), co-immunoprecipitation, immunofluorescence Journal of cell science Medium 25609707
2015 In the absence of RPA, hSSB1 and INTS3 form subnuclear foci, associate with the ATR-ATRIP complex, and recruit it to sites of genomic stress. ATRIP foci formed after RPA depletion are abrogated upon INTS3 depletion, establishing that the hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex. Depletion of hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation. siRNA depletion, co-immunoprecipitation, immunofluorescence (foci), Chk1 phosphorylation assay Nucleic acids research Medium 25916848
2017 hSSB1 can interact with INTS3 even when hSSB1 forms tetramers under oxidizing conditions, establishing that hSSB1 oligomerization does not preclude its interaction with INTS3 in the SOSS1 complex. Solution NMR, biophysical assays, co-immunoprecipitation Nucleic acids research Medium 28609781
2018 INTS3 displays higher affinity toward ssRNA than ssDNA, requires a minimum of 30 nucleotides for binding, and does not bind dsDNA, dsRNA, or RNA:DNA hybrids. The N-terminus of INTS3 mediates protein-protein interactions, while the C-terminus is required for nucleic acid binding. In the reconstituted heterotrimeric complex, INTS3 (but not C9ORF80) affects the nucleic acid-binding ability of hNABP1 and hNABP2, suggesting INTS3 regulates their biological function. EMSA, GST pulldown, recombinant protein purification, gel filtration The Biochemical journal High 29150435
2020 The crystal structure of the Ints3 C-terminal domain reveals a HEAT-repeat superhelical fold that forms a stable dimer. The C-terminal dimer has a basic groove that binds ssRNA/ssDNA and a separate surface of conserved residues that binds INTS6. Dimerization is required for nucleic acid binding but not for INTS6 binding. In vitro experiments showed that INTS6 interaction is critical for maintaining SSB1 protein level. X-ray crystallography, mutagenesis, EMSA, co-immunoprecipitation, in vitro protein stability assay in HEK293T cells The Journal of biological chemistry High 33434574
2021 The crystal structure of the INTS3 C-terminus (INTS3c) in complex with the INTS6 C-terminus (INTS6c) at 2.4 Å resolution reveals that two INTS3c subunits dimerize and interact with INTS6c via conserved residues. INTS3c dimerization is important for recognizing longer ssDNA. Perturbation of INTS3c dimerization and disruption of the INTS3c/INTS6c interaction impair DSB repair. X-ray crystallography, biochemical binding assays, mutagenesis, DSB repair functional assay Cell discovery High 34400606
2022 PARP1 binds directly to INTS3 (IntS3) via PARP1's C-terminal domain interacting with INTS3's C-terminal domain. The chromatin occupancy of INTS3 along PARP1 target genes mimics PARP1 occupancy. Knockdown of PARP1 results in differential chromatin association and gene occupancy of INTS3, and this effect is due to the physical presence of PARP1 rather than its PARylation activity. Co-immunoprecipitation (in vivo and in vitro), ChIP-seq, siRNA knockdown Cells Medium 36291070
2023 The damage-activated tyrosine kinase c-Abl phosphorylates hSSB1, enabling its interaction with tyrosine-1-phosphorylated RNA Pol II (Y1P RNAPII) at DSBs. The trimeric SOSS1 complex (hSSB1, INTS3, c9orf80) binds to Y1P RNAPII in response to DNA damage in an R-loop-dependent manner, and the complex exhibits strong affinity for R-loops. The SOSS1 complex and RNAPII form dynamic liquid-like (liquid-liquid phase separation) repair compartments at DSBs, and depletion of the SOSS1 complex impairs DNA repair. Co-immunoprecipitation, in vitro binding assay, immunofluorescence, live-cell imaging (liquid droplet/phase separation assays), siRNA depletion with DNA repair readouts Cell reports Medium 38039132
2023 INTS3 interacts with Nbs1 (of the MRN complex) via a phosphorylation-dependent mechanism: the forkhead-associated (FHA) domain of Nbs1 binds INTS3 at phospho-Threonine 592, with contributions from Serine 590. This interaction provides a mechanism for MRN complex recruitment to DSBs via INTS3. In silico modeling, biochemical binding assays (pulldown), phosphopeptide binding assays, functional cellular assays Protein science Medium 37705456
2024 Cryo-EM structures of the complete Integrator-PP2A complex reveal that the previously unresolved INTS3 subunit and associated SOSS factors, in the post-termination complex state, occupy a position that prevents Pol II rebinding to Integrator after transcription termination. Cryo-electron microscopy (three structures in different functional states) Nature High 38570683
2024 INTS6 associates with the heterotrimeric SOSS1 complex (INTS3, INIP/c9orf80, hSSB1) to form a tetrameric SOSS1 complex. INTS6 binds to DNA:RNA hybrids, promotes PP2A recruitment to DSBs to facilitate dephosphorylation of RNAPII, prevents accumulation of damage-associated RNA transcripts (DARTs), and promotes senataxin (SETX) recruitment to DSBs for R-loop resolution. Co-immunoprecipitation, in vitro binding assays, immunofluorescence, functional assays (RNAPII phosphorylation, R-loop accumulation, SETX recruitment) Nucleic acids research Medium 39445827
2024 INTS3 deletion triggers apoptosis in colorectal cancer cells. INTS3 destabilizes pro-apoptotic gene transcripts, contributing to cancer cell survival. INTS3 loss delays CRC cell growth in vivo, identifying INTS3 as an RNA-binding protein with an anti-apoptotic role in CRC. CRISPR-Cas9 screen, siRNA knockdown, RNA sequencing, in vivo tumor growth assay, nanoparticle-mediated knockdown iScience Medium 38665208
2022 Knockdown of SPT6 causes loss of INTS3 from U2 snRNA genes, indicating SPT6 is required for INTS3 recruitment/retention at snRNA gene loci. ChIP-seq, ChIP-qPCR, siRNA knockdown Biomolecules Low 35625631

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2019 Coordinated alterations in RNA splicing and epigenetic regulation drive leukaemogenesis. Nature 184 31578525
2009 SOSS complexes participate in the maintenance of genomic stability. Molecular cell 136 19683501
2015 The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell research 125 25675981
2009 HSSB1 and hSSB2 form similar multiprotein complexes that participate in DNA damage response. The Journal of biological chemistry 95 19605351
2009 INTS3 controls the hSSB1-mediated DNA damage response. The Journal of cell biology 80 19786574
2024 Structural basis of Integrator-dependent RNA polymerase II termination. Nature 53 38570683
2013 A core hSSB1-INTS complex participates in the DNA damage response. Journal of cell science 44 23986477
2008 CREB3L4, INTS3, and SNAPAP are targets for the 1q21 amplicon frequently detected in hepatocellular carcinoma. Cancer genetics and cytogenetics 44 18068530
2013 Single strand DNA binding proteins 1 and 2 protect newly replicated telomeres. Cell research 29 23459151
2021 Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair. Cell discovery 22 34400606
2015 Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response. Journal of cell science 20 25609707
2020 Structural basis for multifunctional roles of human Ints3 C-terminal domain. The Journal of biological chemistry 16 33434574
2018 Biochemical characterization of INTS3 and C9ORF80, two subunits of hNABP1/2 heterotrimeric complex in nucleic acid binding. The Biochemical journal 14 29150435
2023 The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell reports 13 38039132
2017 A data-driven structural model of hSSB1 (NABP2/OBFC2B) self-oligomerization. Nucleic acids research 12 28609781
2015 RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling. Nucleic acids research 9 25916848
2016 Replication Protein A (RPA) deficiency activates the Fanconi anemia DNA repair pathway. Cell cycle (Georgetown, Tex.) 8 27398742
2024 Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks. Nucleic acids research 7 39445827
2022 PARP1's Involvement in RNA Polymerase II Elongation: Pausing and Releasing Regulation through the Integrator and Super Elongation Complex. Cells 7 36291070
2024 CRISPR-Cas9 screening identifies INTS3 as an anti-apoptotic RNA-binding protein and therapeutic target for colorectal cancer. iScience 5 38665208
2019 GATAD2B Gene Microdeletion Causing Intellectual Disability Autosomal Dominant Type 18: Case Report and Review of the Literature. Molecular syndromology 5 31602190
2023 The molecular details of a novel phosphorylation-dependent interaction between MRN and the SOSS complex. Protein science : a publication of the Protein Society 4 37705456
2022 CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. Biomolecules 3 35625631
2025 Characteristics and genomics study of Salmonella isolates in retail chicken in Shaanxi, China: Focus on comparative genomics analysis of S. Kentucky and S. enteritidis isolates from Shaanxi with those from elsewhere in China. International journal of food microbiology 1 41330090
2024 Targeting the hSSB1-INTS3 Interface: A Computational Screening Driven Approach to Identify Potential Modulators. ACS omega 1 38405517
2024 Integrator Complex Subunit 3 Knockdown Has Minimal Effect on Lytic Herpes Simplex Virus Type-1 Infection in Fibroblast Cells. microPublication biology 1 38817634

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