6R92 | pdb_00006r92

Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
H [auth E]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
D [auth A]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
J [auth G]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
F [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
L [auth K]SCOP2B SuperfamilyWD40 repeat-like 8052530 3001694 SCOP2B (2022-06-29)
L [auth K]SCOP2B SuperfamilyWD40 repeat-like 8052530 3001694 SCOP2B (2022-06-29)
L [auth K]SCOP2B SuperfamilyWD40 repeat-like 8051194 3001694 SCOP2B (2022-06-29)
I [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
E [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth L]DAOe6r92L1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
H [auth E]DAOe6r92E1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
D [auth A]DAOe6r92A1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
J [auth G]DAOe6r92G1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
F [auth C]DAOe6r92C1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
L [auth K]DAOe6r92K1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
K [auth H]DAOe6r92H1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
G [auth D]DAOe6r92D1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
I [auth F]DAOe6r92F1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)
E [auth B]DAOe6r92B1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: DAOECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth L]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
D [auth A],
H [auth E]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
F [auth C],
J [auth G]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
L [auth K]PF10433RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)RSE1/DDB1/CPSF1 first beta-propeller- Repeat
L [auth K]PF03178CPSF A subunit region (CPSF_A)CPSF A subunit region- Repeat
E [auth B],
I [auth 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
C [auth L]DNA damage-binding protein 2
D [auth A],
H [auth E]
Histone H3.1
F [auth C],
J [auth G]
Histone H2A type 1-B/E
L [auth K]DNA damage-binding protein 1,DNA damage-binding protein 1
G [auth D],
K [auth H]
Histone H2B type 1-J
E [auth B],
I [auth F]
Histone H4
B [auth J]Human alpha-satellite DNA (145-MER) with abasic sites at positions 93-94---
A [auth I]Human alpha-satellite DNA (145-MER)---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth L]IPR019775WD40 repeat, conserved siteConserved Site
C [auth L]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
C [auth L]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
C [auth L]IPR001680WD40 repeatRepeat
C [auth L]IPR033312DNA damage-binding protein 2Family
D [auth A],
H [auth E]
IPR009072Histone-foldHomologous Superfamily
D [auth A],
H [auth E]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth A],
H [auth E]
IPR000164Histone H3/CENP-AFamily
F [auth C],
J [auth G]
IPR009072Histone-foldHomologous Superfamily
F [auth C],
J [auth G]
IPR002119Histone H2AFamily
F [auth C],
J [auth G]
IPR007125Core Histone H2A/H2B/H3 domainDomain
F [auth C],
J [auth G]
IPR032454Histone H2A, C-terminal domainDomain
F [auth C],
J [auth G]
IPR032458Histone H2A conserved siteConserved Site
L [auth K]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
L [auth K]IPR058543RSE1/DDB1/CPSF1, second beta-propellerDomain
L [auth K]IPR004871RSE1/DDB1/CPSF1, C-terminalDomain
L [auth K]IPR050358RSE1/DDB1/CPSF1Family
L [auth K]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
L [auth K]IPR018846RSE1/DDB1/CPSF1, first beta-propellerDomain
G [auth D],
K [auth H]
IPR009072Histone-foldHomologous Superfamily
G [auth D],
K [auth H]
IPR000558Histone H2BFamily
G [auth D],
K [auth H]
IPR007125Core Histone H2A/H2B/H3 domainDomain
G [auth D],
K [auth H]
IPR055333Histone H2B, conserved siteConserved Site
E [auth B],
I [auth F]
IPR009072Histone-foldHomologous Superfamily
E [auth B],
I [auth F]
IPR035425CENP-T/Histone H4, histone foldDomain
E [auth B],
I [auth F]
IPR001951Histone H4Family
E [auth B],
I [auth F]
IPR019809Histone H4, conserved siteConserved Site
E [auth B],
I [auth F]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
C [auth L]PharosQ92466
D [auth A],
H [auth E]
PharosP68431
F [auth C],
J [auth G]
PharosP04908
L [auth K]PharosQ16531
G [auth D],
K [auth H]
PharosP06899
E [auth B],
I [auth F]
PharosP62805