6KIX | pdb_00006kix

Cryo-EM structure of human MLL1-NCP complex, binding mode1


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AHistonee6kixA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
EHistonee6kixE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
BHistone_1e6kixB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
FHistone_1e6kixF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
CHistone_1e6kixC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
GHistone_1e6kixG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: Histone_1ECOD (1.6)
DHistonee6kixD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
HHistonee6kixH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: HistoneECOD (1.6)
L [auth K]SETe6kixK1 A: beta barrelsX: beta-clipH: SET domain-like (From Topology)T: SET domain-likeF: SETECOD (1.6)
M [auth R]ANAPC4_WD40_18e6kixR1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: ANAPC4_WD40_18ECOD (1.6)
N [auth T]SPRYe6kixT1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: SPRYECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
C, G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
K [auth N]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
L [auth K]PF00856SET domain (SET)SET domain- Family
M [auth R]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
N [auth T]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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3 -
B, F
Histone H4
C, G
Histone H2A
D, H
Histone H2B 1.1 -
DNA (145-MER)---
DNA (145-MER)---
K [auth N]Retinoblastoma-binding protein 5
L [auth K]Histone-lysine N-methyltransferase 2A
M [auth R]WD repeat-containing protein 5
N [auth T]Set1/Ash2 histone methyltransferase complex subunit ASH2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR000164Histone H3/CENP-AFamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR001951Histone H4Family
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR019809Histone H4, conserved siteConserved Site
B, F
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
C, G
IPR009072Histone-foldHomologous Superfamily
C, G
IPR002119Histone H2AFamily
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
C, G
IPR007125Core Histone H2A/H2B/H3 domainDomain
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR055333Histone H2B, conserved siteConserved Site
D, H
IPR000558Histone H2BFamily
D, H
IPR007125Core Histone H2A/H2B/H3 domainDomain
K [auth N]IPR037850Retinoblastoma-binding protein 5/Swd1Family
K [auth N]IPR001680WD40 repeatRepeat
K [auth N]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
L [auth K]IPR001965Zinc finger, PHD-typeDomain
L [auth K]IPR046341SET domain superfamilyHomologous Superfamily
L [auth K]IPR001214SET domainDomain
L [auth K]IPR044133KMT2A, PHD domain 3Domain
L [auth K]IPR003616Post-SET domainDomain
L [auth K]IPR034732Extended PHD (ePHD) domainDomain
L [auth K]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
L [auth K]IPR036427Bromodomain-like superfamilyHomologous Superfamily
L [auth K]IPR003888FY-rich, N-terminalConserved Site
L [auth K]IPR001487BromodomainDomain
L [auth K]IPR002857Zinc finger, CXXC-typeDomain
L [auth K]IPR019787Zinc finger, PHD-fingerDomain
L [auth K]IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
L [auth K]IPR041958KMT2A, ePHD domainDomain
L [auth K]IPR047219Histone-lysine N-methyltransferase 2A/2B, SET domainDomain
L [auth K]IPR042025KMT2A, PHD domain 2Domain
L [auth K]IPR003889FY-rich, C-terminalConserved Site
L [auth K]IPR016569Methyltransferase, trithoraxFamily
L [auth K]IPR042023KMT2A, PHD domain 1Domain
M [auth R]IPR019775WD40 repeat, conserved siteConserved Site
M [auth R]IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
M [auth R]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
M [auth R]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
M [auth R]IPR001680WD40 repeatRepeat
N [auth T]IPR053835Set1/Ash2 histone methyltransferase complex subunit ASH2-like, winged-helixDomain
N [auth T]IPR001870B30.2/SPRY domainDomain
N [auth T]IPR013320Concanavalin A-like lectin/glucanase domain superfamilyHomologous Superfamily
N [auth T]IPR043136B30.2/SPRY domain superfamilyHomologous Superfamily
N [auth T]IPR049455Set1/Ash2 histone methyltransferase complex subunit ASH2-like, PHD zinc fingerDomain
N [auth T]IPR037353Histone methyltransferase complex subunit ASH2Family
N [auth T]IPR003877SPRY domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
K [auth N]PharosQ15291
L [auth K]PharosQ03164
M [auth R]PharosP61964
N [auth T]PharosQ9UBL3