7D20 | pdb_00007d20

Cryo-EM structure of SET8-CENP-A-nucleosome complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
GSCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
D [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
B [auth E]SCOP2B SuperfamilyCore histone-like 8070539 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8070539 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
J [auth K]V-sete7d20K1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
K [auth H]V-sete7d20H1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
E [auth D]V-sete7d20D1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
GV-sete7d20G1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
D [auth C]V-sete7d20C1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
FV-sete7d20F1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
C [auth B]V-sete7d20B1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
B [auth E]V-sete7d20E1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)
AV-sete7d20A1 A: a/b three-layered sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth K]PF00856SET domain (SET)SET domain- Family
D [auth C],
G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
J [auth K]Isoform 2 of N-lysine methyltransferase KMT5A
I [auth J]DNA (145-MER)---
H [auth I]DNA (145-MER)---
E [auth D],
K [auth H]
Histone H2B type 1-J
D [auth C],
G
Histone H2A type 1-B/E
C [auth B],
F
Histone H4
A,
B [auth E]
Histone H3-like centromeric protein A

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
J [auth K]PharosQ9NQR1
E [auth D],
K [auth H]
PharosP06899
D [auth C],
G
PharosP04908
C [auth B],
F
PharosP62805
A,
B [auth E]
PharosP49450