8HQY | pdb_00008hqy

Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
J [auth U]SCOP2B SuperfamilyUbiquitin-like 8101457 3000157 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth U]PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
I [auth S]PF09514SSXRD motif (SSXRD)SSXRD motif- Motif
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
D, H
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
A, E
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
K [auth I]DNA (137-MER)---
J [auth U]Polyubiquitin-B (Fragment)
I [auth S]Protein SSX2-
Histone H2A type 1-B/E
Histone H4
D, H
Histone H2B type 1-K
Histone H2A type 1-B/E
Histone H4 (Fragment)
L [auth J]DNA (136-MER)---
A, E
Histone H3

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth U]IPR019954Ubiquitin conserved siteConserved Site
J [auth U]IPR050158Ubiquitin and ubiquitin-likeFamily
J [auth U]IPR000626Ubiquitin-like domainDomain
J [auth U]IPR019956Ubiquitin domainDomain
J [auth U]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
I [auth S]IPR003655Ancestral KRAB domainDomain
I [auth S]IPR001909Krueppel-associated boxDomain
I [auth S]IPR019041SSXRD motifConserved Site
I [auth S]IPR036051Krueppel-associated box domain superfamilyHomologous Superfamily
IPR009072Histone-foldHomologous Superfamily
IPR002119Histone H2AFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR032454Histone H2A, C-terminal domainDomain
IPR032458Histone H2A conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR035425CENP-T/Histone H4, histone foldDomain
IPR001951Histone H4Family
IPR019809Histone H4, conserved siteConserved Site
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR000558Histone H2BFamily
D, H
IPR007125Core Histone H2A/H2B/H3 domainDomain
D, H
IPR055333Histone H2B, conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR002119Histone H2AFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR032454Histone H2A, C-terminal domainDomain
IPR032458Histone H2A conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR035425CENP-T/Histone H4, histone foldDomain
IPR001951Histone H4Family
IPR019809Histone H4, conserved siteConserved Site
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
A, E
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
J [auth U]PharosP0CG47
I [auth S]PharosQ16385
PharosP04908
PharosP62805
D, H
PharosO60814
PharosP04908
PharosP62805
A, E
PharosQ71DI3