7LYC | pdb_00007lyc

Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777)


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
I [auth K]d7lyck1 Alpha and beta proteins (a+b) beta-Grasp (ubiquitin-like) Ubiquitin-like Ubiquitin-related Ubiquitin Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
I [auth K]d7lyck2 Artifacts Tags Tags Tags N-terminal Tags Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
L [auth G]d7lycg1 All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
L [auth G]d7lycg2 Artifacts Tags Tags Tags N-terminal Tags Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
K [auth C]d7lycc1 All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
K [auth C]d7lycc2 Artifacts Tags Tags Tags N-terminal Tags Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
F [auth H]d7lych_ All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
C [auth D]d7lycd_ All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
E [auth F]d7lycf_ All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Bd7lycb_ All alpha proteins Histone-fold Histone-fold Nucleosome core histones automated matches Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth K]SCOP2B SuperfamilyUbiquitin-like 8101457 3000157 SCOP2B (2022-06-29)
L [auth G]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
K [auth C]SCOP2B SuperfamilyCore histone-like 8039342 3001387 SCOP2B (2022-06-29)
J [auth N]SCOP2B SuperfamilyBRCT domain-like 8004132 3000159 SCOP2B (2022-06-29)
J [auth N]SCOP2B SuperfamilyAnkyrin repeat 8057709 3000154 SCOP2B (2022-06-29)
J [auth N]SCOP2B SuperfamilyBRCT domain-like 8091657 3000159 SCOP2B (2022-06-29)
E [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
D [auth E]SCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth K]ubiquitin_1e7lycK1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: ubiquitin_1ECOD (1.6)
L [auth G]Histone_1e7lycG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
K [auth C]Histone_1e7lycC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
J [auth N]Ank_2e7lycN1 A: alpha superhelicesX: Repetitive alpha hairpinsH: Ankyrin repeat (From Topology)T: Ankyrin repeatF: Ank_2ECOD (1.6)
J [auth N]PTCB-BRCTe7lycN3 A: a/b three-layered sandwichesX: BRCT domain (From Topology)H: BRCT domain (From Topology)T: BRCT domainF: PTCB-BRCTECOD (1.6)
F [auth H]Histonee7lycH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
C [auth D]Histonee7lycD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
E [auth F]Histone_1e7lycF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
BHistone_1e7lycB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
D [auth E]Histonee7lycE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
AHistonee7lycA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
I [auth K]3.10.20.90 Alpha Beta Roll Ubiquitin-like (UB roll) Phosphatidylinositol 3-kinase Catalytic SubunitCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth K]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
K [auth C],
L [auth G]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
K [auth C],
L [auth G]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
J [auth N]PF00023Ankyrin repeat (Ank)Ankyrin repeat- Repeat
J [auth N]PF00533BRCA1 C Terminus (BRCT) domain (BRCT)BRCA1 C Terminus (BRCT) domainThe BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- ...The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].
Domain
B,
E [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
I [auth K]Ubiquitin
K [auth C],
L [auth G]
Histone H2A type 1-B/E
J [auth N]BRCA1-associated RING domain protein 1
H [auth J]DNA (146-MER)---
G [auth I]DNA (147-MER)---
C [auth D],
F [auth H]
Histone H2B type 1-J
B,
E [auth F]
Histone H4
A,
D [auth E]
Histone H3.1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth K]IPR019954Ubiquitin conserved siteConserved Site
I [auth K]IPR050158Ubiquitin and ubiquitin-likeFamily
I [auth K]IPR000626Ubiquitin-like domainDomain
I [auth K]IPR019956Ubiquitin domainDomain
I [auth K]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
K [auth C],
L [auth G]
IPR009072Histone-foldHomologous Superfamily
K [auth C],
L [auth G]
IPR002119Histone H2AFamily
K [auth C],
L [auth G]
IPR007125Core Histone H2A/H2B/H3 domainDomain
K [auth C],
L [auth G]
IPR032454Histone H2A, C-terminal domainDomain
K [auth C],
L [auth G]
IPR032458Histone H2A conserved siteConserved Site
J [auth N]IPR039503BARD1, Zinc finger, RING-typeDomain
J [auth N]IPR002110Ankyrin repeatRepeat
J [auth N]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
J [auth N]IPR001841Zinc finger, RING-typeDomain
J [auth N]IPR036770Ankyrin repeat-containing domain superfamilyHomologous Superfamily
J [auth N]IPR001357BRCT domainDomain
J [auth N]IPR036420BRCT domain superfamilyHomologous Superfamily
J [auth N]IPR017907Zinc finger, RING-type, conserved siteConserved Site
C [auth D],
F [auth H]
IPR009072Histone-foldHomologous Superfamily
C [auth D],
F [auth H]
IPR000558Histone H2BFamily
C [auth D],
F [auth H]
IPR007125Core Histone H2A/H2B/H3 domainDomain
C [auth D],
F [auth H]
IPR055333Histone H2B, conserved siteConserved Site
B,
E [auth F]
IPR009072Histone-foldHomologous Superfamily
B,
E [auth F]
IPR035425CENP-T/Histone H4, histone foldDomain
B,
E [auth F]
IPR001951Histone H4Family
B,
E [auth F]
IPR019809Histone H4, conserved siteConserved Site
B,
E [auth F]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
A,
D [auth E]
IPR009072Histone-foldHomologous Superfamily
A,
D [auth E]
IPR007125Core Histone H2A/H2B/H3 domainDomain
A,
D [auth E]
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
I [auth K]PharosP0CG47
K [auth C],
L [auth G]
PharosP04908
J [auth N]PharosQ99728
C [auth D],
F [auth H]
PharosP06899
B,
E [auth F]
PharosP62805
A,
D [auth E]
PharosP68431