Affinage

INTS3

Integrator complex subunit 3 · UniProt Q68E01

Length
1043 aa
Mass
118.1 kDa
Annotated
2026-04-28
25 papers in source corpus 7 papers cited in narrative 7 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

INTS3 is a scaffold subunit of the SOSS1 complex (INTS3–hSSB1–C9ORF80) that coordinates single-stranded nucleic acid recognition with DNA damage signaling and repair. Its C-terminal HEAT-repeat domain dimerizes to form a basic groove that binds ssDNA and ssRNA (preferring ssRNA, minimum ~30 nt), while its N-terminal domain mediates interaction with hSSB1/NABP2, and a conserved surface on the C-terminal dimer engages INTS6 to maintain hSSB1 protein levels (PMID:33434574, PMID:34400606, PMID:29150435). The INTS3-containing SOSS1 complex is recruited to DNA double-strand breaks where it activates ATM signaling, promotes RAD51-dependent homologous recombination, and can also initiate an alternative ATR–Chk1 pathway in the absence of RPA (PMID:19786574, PMID:25916848). INTS3 additionally functions as an RNA-binding protein that destabilizes pro-apoptotic transcripts, and its deletion triggers apoptosis in colorectal cancer cells and suppresses tumor growth in vivo (PMID:38665208).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2009 High

    Identification of INTS3 as a core member of a novel ssDNA-sensing complex (SOSS1) established that it functions beyond the Integrator complex, directly linking it to ATM activation and RAD51-mediated homologous recombination repair.

    Evidence Tandem affinity purification of hSSB1 complexes followed by ATM activation and RAD51 foci assays in human cells

    PMID:19786574

    Open questions at the time
    • Structural basis of INTS3–hSSB1 interaction unknown
    • Whether INTS3 directly contacts DNA or acts solely as a scaffold was unresolved
    • Contribution of C9ORF80 to complex function undefined
  2. 2015 Medium

    Demonstrating that INTS3 and hSSB1 can recruit ATRIP and activate ATR–Chk1 signaling independently of RPA revealed a second, parallel DNA damage checkpoint pathway mediated by the SOSS1 complex.

    Evidence siRNA knockdown of RPA, hSSB1/2, and INTS3 with epistasis analysis of Chk1 phosphorylation and ATRIP foci in human cells

    PMID:25916848

    Open questions at the time
    • Physiological contexts where this alternative ATR pathway dominates remain unclear
    • Direct physical interaction between INTS3 and ATRIP not demonstrated
  3. 2018 Medium

    Biochemical reconstitution showed that INTS3 itself is a nucleic acid-binding protein with preference for ssRNA over ssDNA, resolving whether INTS3 contributes directly to substrate recognition or only serves as a scaffold.

    Evidence EMSA and GST pulldown with recombinant INTS3 and reconstituted heterotrimeric SOSS1 complex

    PMID:29150435

    Open questions at the time
    • Structural basis of ssRNA preference not determined
    • In vivo RNA targets of INTS3 unknown
    • Role of INTS3 nucleic acid binding in DSB repair versus RNA metabolism not distinguished
  4. 2020 High

    Crystal structure of the INTS3 C-terminal domain revealed a HEAT-repeat dimer whose basic groove binds ssDNA/ssRNA, while a distinct conserved surface engages INTS6, providing the first structural framework for understanding SOSS1 assembly and nucleic acid recognition.

    Evidence X-ray crystallography at atomic resolution, EMSA, mutagenesis, and HEK 293T protein stability assays

    PMID:33434574

    Open questions at the time
    • Full-length SOSS1 complex structure not available
    • How INTS6 binding stabilizes hSSB1 protein levels mechanistically is unclear
  5. 2021 High

    A higher-resolution structure of the INTS3–INTS6 interface showed that INTS3 dimerization is functionally required for recognizing longer ssDNA substrates and for proficient DSB repair, linking structural oligomerization to genome maintenance.

    Evidence 2.4 Å crystal structure, mutagenesis of dimer and INTS6-binding interfaces, DSB repair functional assays

    PMID:34400606

    Open questions at the time
    • Whether INTS3 dimerization status is regulated in response to DNA damage is unknown
    • Relationship between INTS3 dimer-mediated ssDNA binding and ATM/ATR activation not mechanistically connected
  6. 2024 Medium

    Discovery of an RNA-regulatory role for INTS3 — destabilizing pro-apoptotic transcripts to promote cancer cell survival — expanded its functional scope beyond DNA repair to post-transcriptional gene regulation.

    Evidence CRISPR-Cas9 screen in colorectal cancer cells, RNA-seq, apoptosis assays, and xenograft models

    PMID:38665208

    Open questions at the time
    • Specific RNA targets and degradation pathway through which INTS3 acts are not fully defined
    • Whether this RNA-regulatory function depends on the SOSS1 complex or on INTS3 alone is unresolved
    • Generalizability beyond colorectal cancer not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the structure of the full SOSS1 holocomplex, the mechanism by which INTS3 selectively destabilizes RNA transcripts, whether INTS3 dimerization is dynamically regulated during the DNA damage response, and how its dual DNA repair and RNA regulatory functions are coordinated.
  • No full-length SOSS1 complex structure available
  • Mechanism of INTS3-mediated mRNA destabilization unknown
  • Regulation of INTS3 dimerization in vivo not characterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0003723 RNA binding 3 GO:0060090 molecular adaptor activity 2
Localization
GO:0005694 chromosome 3 GO:0005634 nucleus 2
Pathway
R-HSA-73894 DNA Repair 3
Partners
ATRIPC9ORF80INTS6NABP2
Complex memberships
SOSS1 (INTS3–hSSB1–C9ORF80)

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 INTS3 forms a complex with hSSB1 (human single-stranded DNA binding protein 1) and a subset of Integrator complex subunits, along with the uncharacterized protein MISE/C9ORF80, identified by tandem affinity purification. This INTS3-MISE-hSSB1 complex plays a key role in ATM activation and RAD51 recruitment to DNA damage foci, and INTS3 controls hSSB1 levels transcriptionally. Tandem affinity purification, co-purification, ATM activation and RAD51 foci assays The Journal of cell biology High 19786574
2021 The C-terminus of INTS3 dimerizes and interacts with the C-terminus of INTS6 via conserved residues, as revealed by a 2.4 Å crystal structure. INTS3 dimerization is required for recognizing longer ssDNA, and perturbation of INTS3 dimerization or disruption of the INTS3/INTS6 interaction impairs double-strand break (DSB) repair. X-ray crystallography, biochemical binding assays, mutagenesis, DSB repair functional assays Cell discovery High 34400606
2020 The C-terminal domain of INTS3 adopts a HEAT-repeat superhelical fold and forms a stable dimer. A basic groove on the dimer binds ssRNA/ssDNA (requiring dimerization), while a cluster of conserved residues on the opposite face binds INTS6. INTS6 interaction is critical for maintaining SSB1 protein levels in cells. X-ray crystallography, EMSA, mutagenesis, HEK 293T cell-based protein level assays The Journal of biological chemistry High 33434574
2018 Recombinant INTS3 binds ssRNA with higher affinity than ssDNA and requires a minimum of 30 nucleotides for binding; it 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. INTS3 modulates the nucleic acid-binding ability of hNABP1/2 within the heterotrimeric complex, whereas C9ORF80 does not. EMSA (electrophoretic mobility shift assay), GST pulldown, recombinant protein purification, reconstituted heterotrimeric complex The Biochemical journal Medium 29150435
2015 In the absence of RPA, hSSB1 and its partner INTS3 form sub-nuclear foci, associate with the ATR-ATRIP complex, and recruit it to sites of genomic stress. INTS3 depletion abrogates ATRIP foci formed after RPA depletion. Depletion of hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation, indicating the hSSB1/2-INTS3 complex can initiate an alternative ATR signaling pathway requiring TopBP1 and the Rad9-Rad1-Hus1 complex. siRNA knockdown, immunofluorescence foci assays, co-immunoprecipitation, Chk1 phosphorylation assays Nucleic acids research Medium 25916848
2024 INTS3 acts as an RNA-binding protein that destabilizes pro-apoptotic gene transcripts, thereby promoting colorectal cancer cell survival. INTS3 deletion triggers apoptosis in CRC cells in vitro and delays tumor growth in vivo. CRISPR-Cas9 pooled screen, RNA sequencing, in vitro apoptosis assays, in vivo xenograft iScience Medium 38665208
2024 Computational screening identified small molecules that disrupt the INTS3-hSSB1 protein-protein interaction at the hSSB1-binding interface of INTS3; one compound impaired recruitment of both hSSB1 and INTS3 to chromatin following DNA damage, validated by co-immunoprecipitation and immunofluorescence. Molecular docking virtual screening, co-immunoprecipitation, immunofluorescence, molecular dynamics simulation ACS omega Low 38405517

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1992 Expression of an activated Notch-related int-3 transgene interferes with cell differentiation and induces neoplastic transformation in mammary and salivary glands. Genes & development 320 1372276
1992 Mouse mammary tumor gene int-3: a member of the notch gene family transforms mammary epithelial cells. Journal of virology 237 1312643
1994 Three genes in the human MHC class III region near the junction with the class II: gene for receptor of advanced glycosylation end products, PBX2 homeobox gene and a notch homolog, human counterpart of mouse mammary tumor gene int-3. Genomics 210 7835890
1997 The mouse mammary tumor associated gene INT3 is a unique member of the NOTCH gene family (NOTCH4). Oncogene 166 9150355
1996 Expression of a truncated Int3 gene in developing secretory mammary epithelium specifically retards lobular differentiation resulting in tumorigenesis. Cancer research 155 8620493
1987 A new common integration region (int-3) for mouse mammary tumor virus on mouse chromosome 17. Journal of virology 118 3023699
1995 Constitutive expression of a truncated INT3 gene in mouse mammary epithelium impairs differentiation and functional development. Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research 90 7544153
2009 INTS3 controls the hSSB1-mediated DNA damage response. The Journal of cell biology 79 19786574
1997 Proto-oncogene of int-3, a mouse Notch homologue, is expressed in endothelial cells during early embryogenesis. Genes to cells : devoted to molecular & cellular mechanisms 60 9189758
2008 Rbpj conditional knockout reveals distinct functions of Notch4/Int3 in mammary gland development and tumorigenesis. Oncogene 44 18836481
2008 CREB3L4, INTS3, and SNAPAP are targets for the 1q21 amplicon frequently detected in hepatocellular carcinoma. Cancer genetics and cytogenetics 43 18068530
2004 Mammary development and tumorigenesis in mice expressing a truncated human Notch4/Int3 intracellular domain (h-Int3sh). Oncogene 41 15531924
2004 Expression of constitutively active Notch4 (Int-3) modulates myeloid proliferation and differentiation and promotes expansion of hematopoietic progenitors. Leukemia 24 14961038
1997 Gene organization of human NOTCH4 and (CTG)n polymorphism in this human counterpart gene of mouse proto-oncogene Int3. Gene 23 9168133
1994 Insertional mutation of int protooncogenes in the mammary tumors of a new strain of mice derived from the wild in China: normal- and tumor-tissue-specific expression of int-3 transcripts. Virology 23 8030284
2021 Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair. Cell discovery 22 34400606
1999 Intracisternal type A particle-mediated activation of the Notch4/int3 gene in a mouse mammary tumor: generation of truncated Notch4/int3 mRNAs by retroviral splicing events. Journal of virology 18 10233982
1995 A novel non-mouse mammary tumor virus activation of the Int-3 gene in a spontaneous mouse mammary tumor. Journal of virology 17 7494323
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
2006 Kit and PDGFR-alpha activities are necessary for Notch4/Int3-induced tumorigenesis. Oncogene 14 16878155
2017 The ANK repeats of Notch-4/Int3 activate NF-κB canonical pathway in the absence of Rbpj and causes mammary tumorigenesis. Scientific reports 10 29057904
2015 RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling. Nucleic acids research 9 25916848
2024 CRISPR-Cas9 screening identifies INTS3 as an anti-apoptotic RNA-binding protein and therapeutic target for colorectal cancer. iScience 4 38665208
2024 Targeting the hSSB1-INTS3 Interface: A Computational Screening Driven Approach to Identify Potential Modulators. ACS omega 1 38405517