8GRM | pdb_00008grm

Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ESCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8039341 3001387 SCOP2B (2022-06-29)
I [auth M]SCOP2B SuperfamilyRING/U-box like 8079705 3000160 SCOP2B (2022-06-29)
M [auth O]SCOP2B SuperfamilyUbiquitin-like 8101457 3000157 SCOP2B (2022-06-29)
N [auth P]SCOP2B SuperfamilyUBC-like 8040137 3000570 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
EF_UNCLASSIFIEDe8grmE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
AF_UNCLASSIFIEDe8grmA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
FF_UNCLASSIFIEDe8grmF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
BF_UNCLASSIFIEDe8grmB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
GF_UNCLASSIFIEDe8grmG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
CF_UNCLASSIFIEDe8grmC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
DF_UNCLASSIFIEDe8grmD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
HF_UNCLASSIFIEDe8grmH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: F_UNCLASSIFIEDECOD (1.6)
I [auth M]F_UNCLASSIFIEDe8grmM1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: F_UNCLASSIFIEDECOD (1.6)
J [auth N]F_UNCLASSIFIEDe8grmN1 A: few secondary structure elementsX: RING/U-box-likeH: RING/U-box-likeT: RING/U-boxF: F_UNCLASSIFIEDECOD (1.6)
M [auth O]F_UNCLASSIFIEDe8grmO1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: F_UNCLASSIFIEDECOD (1.6)
N [auth P]F_UNCLASSIFIEDe8grmP1 A: a+b two layersX: UBC-likeH: UBC-like (From Topology)T: UBC-likeF: F_UNCLASSIFIEDECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, E
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
B, F
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
C, G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C, G
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
I [auth M]PF13923Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)Zinc finger, C3HC4 type (RING finger)Domain
J [auth N]PF13923Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_2)Zinc finger, C3HC4 type (RING finger)Domain
M [auth O]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
N [auth P]PF00179Ubiquitin-conjugating enzyme (UQ_con)Ubiquitin-conjugating enzymeProteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3
B, F
Histone H4
C, G
Histone H2A type 1-B/E
Histone H2B type 1-K
Histone H2B type 1-K
I [auth M]COMMD3 protein
J [auth N]Ring1B
K [auth I]DNA (144-MER)---
L [auth J]DNA (145-MER)---
M [auth O]Ubiquitin
N [auth P]UbcH5b

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
A, E
IPR000164Histone H3/CENP-AFamily
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR001951Histone H4Family
B, F
IPR019809Histone H4, conserved siteConserved Site
B, F
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
C, G
IPR009072Histone-foldHomologous Superfamily
C, G
IPR002119Histone H2AFamily
C, G
IPR007125Core Histone H2A/H2B/H3 domainDomain
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR000558Histone H2BFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR055333Histone H2B, conserved siteConserved Site
IPR009072Histone-foldHomologous Superfamily
IPR000558Histone H2BFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR055333Histone H2B, conserved siteConserved Site
I [auth M]IPR017907Zinc finger, RING-type, conserved siteConserved Site
I [auth M]IPR032443RAWUL domainDomain
I [auth M]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
I [auth M]IPR001841Zinc finger, RING-typeDomain
J [auth N]IPR043540E3 ubiquitin-protein ligase RING1/RING2Family
J [auth N]IPR017907Zinc finger, RING-type, conserved siteConserved Site
J [auth N]IPR032443RAWUL domainDomain
J [auth N]IPR037937E3 ubiquitin-protein ligase RING2, RAWUL domainDomain
J [auth N]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
J [auth N]IPR001841Zinc finger, RING-typeDomain
M [auth O]IPR019954Ubiquitin conserved siteConserved Site
M [auth O]IPR050158Ubiquitin and ubiquitin-likeFamily
M [auth O]IPR000626Ubiquitin-like domainDomain
M [auth O]IPR019956Ubiquitin domainDomain
M [auth O]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
N [auth P]IPR016135Ubiquitin-conjugating enzyme/RWD-likeHomologous Superfamily
N [auth P]IPR000608Ubiquitin-conjugating (UBC), catalytic core domainDomain
N [auth P]IPR023313Ubiquitin-conjugating enzyme, active siteActive Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, E
PharosP68431
B, F
PharosP62805
C, G
PharosP04908
PharosO60814
PharosO60814
I [auth M]PharosP35226
J [auth N]PharosQ99496
M [auth O]PharosP0CG47
N [auth P]PharosP62837