6C24 | pdb_00006c24

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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

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

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
F [auth M]Actine6c24M1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: ActinECOD (v294.1)
L [auth C]Pkinasee6c24C1 A: a/b three-layered sandwichesX: Protein kinase/SAICAR synthase/ATP-graspH: Protein kinase/SAICAR synthase/ATP-graspT: Protein kinaseF: PkinaseECOD (v294.1)
D [auth K]Actine6c24K1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: ActinECOD (v294.1)
E [auth L]Actine6c24L1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: ActinECOD (v294.1)
G [auth N]Actine6c24N1 A: a/b three-layered sandwichesX: Periplasmic binding protein-like IIH: Rubredoxin-relatedT: Tetrapyrrole methylase C-terminal domainF: ActinECOD (v294.1)
I [auth P]NADHdhe6c24P1 A: a/b three-layered sandwichesX: Family A G protein-coupled receptor-likeH: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit 8 (Nqo8)-relatedF: NADHdhECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
D [auth K],
L [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
D [auth K],
L [auth C]
PF00856SET domain (SET)SET domain- Family
D [auth K],
L [auth C]
PF11616WD repeat binding protein EZH2 (EZH2_WD-Binding)WD repeat binding protein EZH2- Family
E [auth L]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
G [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
G [auth N]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A,
F [auth M],
J [auth Q]
IPR019135Polycomb protein, VEFS-BoxDomain
A,
F [auth M],
J [auth Q]
IPR057540Polycomb protein SUZ12-like, zinc finger domainDomain
C [auth E]IPR003347JmjC domainDomain
C [auth E]IPR003349JmjN domainDomain
C [auth E]IPR001606ARID DNA-binding domainDomain
C [auth E]IPR004198Zinc finger, C5HC2-typeDomain
C [auth E]IPR036431ARID DNA-binding domain superfamilyHomologous Superfamily
D [auth K],
L [auth C]
IPR048358EZH1/2, MCSS domainDomain
D [auth K],
L [auth C]
IPR021654Histone-lysine N-methyltransferase EZH1/EZH2, N-terminalDomain
D [auth K],
L [auth C]
IPR041343Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domainDomain
D [auth K],
L [auth C]
IPR046341SET domain superfamilyHomologous Superfamily
D [auth K],
L [auth C]
IPR001214SET domainDomain
D [auth K],
L [auth C]
IPR045318Histone-lysine N-methyltransferase EZH1/2-likeFamily
D [auth K],
L [auth C]
IPR033467Tesmin/TSO1-like CXC domainDomain
D [auth K],
L [auth C]
IPR044439EZH2, SET domainDomain
D [auth K],
L [auth C]
IPR026489CXC domainDomain
D [auth K],
L [auth C]
IPR041355Pre-SET CXC domainDomain
D [auth K],
L [auth C]
IPR001005SANT/Myb domainDomain
E [auth L]IPR019775WD40 repeat, conserved siteConserved Site
E [auth L]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
E [auth L]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
E [auth L]IPR001680WD40 repeatRepeat
E [auth L]IPR051243Polycomb group WD repeat-containing proteinFamily
G [auth N]IPR050459WD repeat RBAP46/RBAP48/MSI1Family
G [auth N]IPR019775WD40 repeat, conserved siteConserved Site
G [auth N]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
G [auth N]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
G [auth N]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
G [auth N]IPR022052Histone-binding protein RBBP4-like, N-terminalDomain
G [auth N]IPR001680WD40 repeatRepeat
I [auth P]IPR059034AEBP2-like, C-terminal SH3 domainDomain
I [auth P]IPR013087Zinc finger C2H2-typeDomain
I [auth P]IPR036236Zinc finger C2H2 superfamilyHomologous Superfamily
I [auth P]IPR052130AEBP2/jing C2H2-type zinc-fingerFamily
IPR003347JmjC domainDomain
IPR003349JmjN domainDomain
IPR001606ARID DNA-binding domainDomain
IPR004198Zinc finger, C5HC2-typeDomain
IPR036431ARID DNA-binding domain superfamilyHomologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

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

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
K [auth Z]UNK
M3L Parent Component: LYS

RESIDAA0074

PSI-MOD :  N6,N6,N6-trimethyl-L-lysine MOD:00083