6C23 | pdb_00006c23

Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth N]SCOP2B SuperfamilyWD40 repeat-like 8053350 3001694 SCOP2B (2022-06-29)
E [auth M]SCOP2B SuperfamilyVEFS box-like 8090819 3002459 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
H [auth P]UNK_F_TYPEe6c23P1 A: beta barrelsX: SH3H: Chromo domain-like (From Topology)T: Chromo domain-likeF: UNK_F_TYPEECOD (1.6)
F [auth N]ANAPC4_WD40_20e6c23N1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_20ECOD (1.6)
D [auth L]ANAPC4_WD40_5e6c23L1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_5ECOD (1.6)
C [auth K]SETe6c23K1 A: beta barrelsX: beta-clipH: SET domain-like (From Topology)T: SET domain-likeF: SETECOD (1.6)
C [auth K]Myb_DNA-binding_3e6c23K4 A: alpha arraysX: HTHH: HTHT: tri-helicalF: Myb_DNA-binding_3ECOD (1.6)
C [auth K]KOG1079_4the6c23K3 A: few secondary structure elementsX: Zn3Cys9 preSET domain-related (From Topology)H: Zn3Cys9 preSET domain-related (From Topology)T: Zn3Cys9 preSET domain-relatedF: KOG1079_4thECOD (1.6)
C [auth K]KOG1079_3rde6c23K5 A: few secondary structure elementsX: Zn3Cys9 preSET domain-related (From Topology)H: Zn3Cys9 preSET domain-related (From Topology)T: Zn3Cys9 preSET domain-relatedF: KOG1079_3rdECOD (1.6)
C [auth K]KOG1079_2nde6c23K2 A: few secondary structure elementsX: Ezh2 MCSS domain (From Topology)H: Ezh2 MCSS domain (From Topology)T: Ezh2 MCSS domainF: KOG1079_2ndECOD (1.6)
K [auth C]KOG1079_1ste6c23C2 A: alpha arraysX: HTHH: HTHT: tri-helicalF: KOG1079_1stECOD (1.6)
K [auth C]EZH2_WD-Bindinge6c23C1 A: extended segmentsX: Ezh2 N-terminal domain (From Topology)H: Ezh2 N-terminal domain (From Topology)T: Ezh2 N-terminal domainF: EZH2_WD-BindingECOD (1.6)
E [auth M]VEFS-Boxe6c23M1 A: alpha arraysX: lambda integrase-N-likeH: VEFS domain (From Topology)T: VEFS domainF: VEFS-BoxECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
F [auth N]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)
D [auth L]2.130.10.10 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
F [auth N]PF12265Histone-binding protein RBBP4 or subunit C of CAF1 complex (CAF1C_H4-bd)Histone-binding protein RBBP4 or subunit C of CAF1 complex- Repeat
F [auth N]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
D [auth L]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
C [auth K],
K [auth C]
PF18264CXC domain (preSET_CXC)CXC domainThis domain is found to the N-terminus of the SET domain in the EZH2 protein [1]. It is a zinc binding domain. Domain
C [auth K],
K [auth C]
PF00856SET domain (SET)SET domain- Family
C [auth K],
K [auth C]
PF18118Polycomb repressive complex 2 tri-helical domain (PRC2_HTH_1)Polycomb repressive complex 2 tri-helical domainThis domain can be found in the Polycomb repressive complex 2 (PRC2) present in Homo sapiens. Polycomb complexes maintain repressive chromatin states by silencing gene expression. PRC2 does this by methylating lysine 27 of histone H3. This domain mak ...This domain can be found in the Polycomb repressive complex 2 (PRC2) present in Homo sapiens. Polycomb complexes maintain repressive chromatin states by silencing gene expression. PRC2 does this by methylating lysine 27 of histone H3. This domain makes up part of the N-lobe which is involved in regulation [1].
Domain
C [auth K],
K [auth C]
PF11616WD repeat binding protein EZH2 (EZH2_WD-Binding)WD repeat binding protein EZH2- Family
A,
E [auth M],
I [auth Q]
PF09733VEFS-Box of polycomb protein (VEFS-Box)VEFS-Box of polycomb protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
L [auth B]Protein Jumonji
J [auth Z]SUZ12---
H [auth P]Zinc finger protein AEBP2
G [auth O]JARID2-substrate---
F [auth N]Histone-binding protein RBBP4
D [auth L]Polycomb protein EED
C [auth K],
K [auth C]
Histone-lysine N-methyltransferase EZH2
B [auth E]Protein Jumonji
A,
E [auth M],
I [auth Q]
Polycomb protein SUZ12

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
L [auth B]IPR003347JmjC domainDomain
L [auth B]IPR003349JmjN domainDomain
L [auth B]IPR001606ARID DNA-binding domainDomain
L [auth B]IPR004198Zinc finger, C5HC2-typeDomain
L [auth B]IPR036431ARID DNA-binding domain superfamilyHomologous Superfamily
H [auth P]IPR013087Zinc finger C2H2-typeDomain
H [auth P]IPR036236Zinc finger C2H2 superfamilyHomologous Superfamily
H [auth P]IPR052130AEBP2/jing C2H2-type zinc-fingerFamily
F [auth N]IPR050459WD repeat RBAP46/RBAP48/MSI1Family
F [auth N]IPR019775WD40 repeat, conserved siteConserved Site
F [auth N]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
F [auth N]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
F [auth N]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
F [auth N]IPR022052Histone-binding protein RBBP4-like, N-terminalDomain
F [auth N]IPR001680WD40 repeatRepeat
D [auth L]IPR019775WD40 repeat, conserved siteConserved Site
D [auth L]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
D [auth L]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
D [auth L]IPR001680WD40 repeatRepeat
D [auth L]IPR051243Polycomb group WD repeat-containing proteinFamily
C [auth K],
K [auth C]
IPR048358EZH1/2, MCSS domainDomain
C [auth K],
K [auth C]
IPR041343Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domainDomain
C [auth K],
K [auth C]
IPR046341SET domain superfamilyHomologous Superfamily
C [auth K],
K [auth C]
IPR001214SET domainDomain
C [auth K],
K [auth C]
IPR045318Histone-lysine N-methyltransferase EZH1/2-likeFamily
C [auth K],
K [auth C]
IPR033467Tesmin/TSO1-like CXC domainDomain
C [auth K],
K [auth C]
IPR044439EZH2, SET domainDomain
C [auth K],
K [auth C]
IPR026489CXC domainDomain
C [auth K],
K [auth C]
IPR041355Pre-SET CXC domainDomain
C [auth K],
K [auth C]
IPR001005SANT/Myb domainDomain
C [auth K],
K [auth C]
IPR021654Histone-lysine N-methyltransferase EZH1/EZH2Family
B [auth E]IPR003347JmjC domainDomain
B [auth E]IPR003349JmjN domainDomain
B [auth E]IPR001606ARID DNA-binding domainDomain
B [auth E]IPR004198Zinc finger, C5HC2-typeDomain
B [auth E]IPR036431ARID DNA-binding domain superfamilyHomologous Superfamily
A,
E [auth M],
I [auth Q]
IPR019135Polycomb protein, VEFS-BoxDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
L [auth B]PharosQ92833
H [auth P]PharosQ6ZN18
F [auth N]PharosQ09028
D [auth L]PharosO75530
C [auth K],
K [auth C]
PharosQ15910
B [auth E]PharosQ92833
A,
E [auth M],
I [auth Q]
PharosQ15022

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
L [auth B]M3L Parent Component: LYS

RESIDAA0074

PSI-MOD :  N6,N6,N6-trimethyl-L-lysine MOD:00083
J [auth Z]UNK RESIDAA0074