6W5M | pdb_00006w5m

Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth G]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
I [auth K]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
F [auth H]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
J [auth L]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
G [auth I]SCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
K [auth M]SCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
H [auth J]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
L [auth N]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AANAPC4_WD40_6e6w5mA1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_6ECOD (1.6)
BANAPC4_WD40_18e6w5mB1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_18ECOD (1.6)
CSETe6w5mC1 A: beta barrelsX: beta-clipH: SET domain-like (From Topology)T: SET domain-likeF: SETECOD (1.6)
DSPRYe6w5mD1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: SPRYECOD (1.6)
E [auth G]Histonee6w5mG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
I [auth K]Histonee6w5mK1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
F [auth H]Histone_1e6w5mH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
J [auth L]Histone_1e6w5mL1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
G [auth I]Histone_1e6w5mI1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
K [auth M]Histone_1e6w5mM1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
H [auth J]Histonee6w5mJ1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
L [auth N]Histonee6w5mN1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF00856SET domain (SET)SET domain- Family
PF00622SPRY domain (SPRY)SPRY domainSPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].
Domain
F [auth H],
J [auth L]
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
G [auth I],
K [auth M]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Retinoblastoma-binding protein 5
N [auth P]DNA (147-MER)---
WD repeat-containing protein 5
Histone-lysine N-methyltransferase 2A
Set1/Ash2 histone methyltransferase complex subunit ASH2
E [auth G],
I [auth K]
Histone H3.2 -
F [auth H],
J [auth L]
Histone H4
G [auth I],
K [auth M]
Histone H2A type 1
H [auth J],
L [auth N]
Histone H2B 1.1 -
M [auth O]DNA (147-MER)---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR037850Retinoblastoma-binding protein 5/Swd1Family
IPR001680WD40 repeatRepeat
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR019775WD40 repeat, conserved siteConserved Site
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR001680WD40 repeatRepeat
IPR001965Zinc finger, PHD-typeDomain
IPR046341SET domain superfamilyHomologous Superfamily
IPR001214SET domainDomain
IPR044133KMT2A, PHD domain 3Domain
IPR003616Post-SET domainDomain
IPR034732Extended PHD (ePHD) domainDomain
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
IPR036427Bromodomain-like superfamilyHomologous Superfamily
IPR003888FY-rich, N-terminalConserved Site
IPR001487BromodomainDomain
IPR002857Zinc finger, CXXC-typeDomain
IPR019787Zinc finger, PHD-fingerDomain
IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
IPR041958KMT2A, ePHD domainDomain
IPR047219Histone-lysine N-methyltransferase 2A/2B, SET domainDomain
IPR042025KMT2A, PHD domain 2Domain
IPR003889FY-rich, C-terminalConserved Site
IPR016569Methyltransferase, trithoraxFamily
IPR042023KMT2A, PHD domain 1Domain
IPR053835Set1/Ash2 histone methyltransferase complex subunit ASH2-like, winged-helixDomain
IPR001870B30.2/SPRY domainDomain
IPR013320Concanavalin A-like lectin/glucanase domain superfamilyHomologous Superfamily
IPR043136B30.2/SPRY domain superfamilyHomologous Superfamily
IPR049455Set1/Ash2 histone methyltransferase complex subunit ASH2-like, PHD zinc fingerDomain
IPR037353Histone methyltransferase complex subunit ASH2Family
IPR003877SPRY domainDomain
E [auth G],
I [auth K]
IPR009072Histone-foldHomologous Superfamily
E [auth G],
I [auth K]
IPR007125Histone H2A/H2B/H3Domain
E [auth G],
I [auth K]
IPR000164Histone H3/CENP-AFamily
F [auth H],
J [auth L]
IPR009072Histone-foldHomologous Superfamily
F [auth H],
J [auth L]
IPR001951Histone H4Family
F [auth H],
J [auth L]
IPR035425CENP-T/Histone H4, histone foldDomain
F [auth H],
J [auth L]
IPR019809Histone H4, conserved siteConserved Site
F [auth H],
J [auth L]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
G [auth I],
K [auth M]
IPR009072Histone-foldHomologous Superfamily
G [auth I],
K [auth M]
IPR007125Histone H2A/H2B/H3Domain
G [auth I],
K [auth M]
IPR002119Histone H2AFamily
G [auth I],
K [auth M]
IPR032454Histone H2A, C-terminal domainDomain
G [auth I],
K [auth M]
IPR032458Histone H2A conserved siteConserved Site
H [auth J],
L [auth N]
IPR009072Histone-foldHomologous Superfamily
H [auth J],
L [auth N]
IPR007125Histone H2A/H2B/H3Domain
H [auth J],
L [auth N]
IPR055333Histone H2B, conserved siteConserved Site
H [auth J],
L [auth N]
IPR000558Histone H2BFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
PharosQ15291
PharosP61964
PharosQ03164
PharosQ9UBL3