8OSK

Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCore histone-like8039340 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like8039340 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like8070545 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like8070545 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like8039342 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like8039342 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF00125e8oskA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
EPF00125e8oskE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
BPF15511e8oskB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
FPF15511e8oskF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
CPF00125,PF16211e8oskC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
GPF00125,PF16211e8oskG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
DPF00125e8oskD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
HPF00125e8oskH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
K [auth M]PF00010e8oskM1 A: alpha duplicates or obligate multimersX: HLH-likeH: HLH, helix-loop-helix DNA-binding domain (From Topology)T: HLH, helix-loop-helix DNA-binding domainF: PF00010ECOD (1.6)
K [auth M]PF00989e8oskM2 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: PF00989ECOD (1.6)
K [auth M]PF14598e8oskM3 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: PF14598ECOD (1.6)
L [auth N]PF00010e8oskN3 A: alpha duplicates or obligate multimersX: HLH-likeH: HLH, helix-loop-helix DNA-binding domain (From Topology)T: HLH, helix-loop-helix DNA-binding domainF: PF00010ECOD (1.6)
L [auth N]PF00989e8oskN2 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: PF00989ECOD (1.6)
L [auth N]PF14598e8oskN1 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: PF14598ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, E
PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
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
C, G
PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
D, H
PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
K [auth M]PF00989PAS fold (PAS)PAS foldThe PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (M ...The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Domain
K [auth M]PF00010Helix-loop-helix DNA-binding domain (HLH)Helix-loop-helix DNA-binding domain- Domain
K [auth M]PF14598PAS domain (PAS_11)PAS domainThis family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6) [1].Domain
L [auth N]PF00989PAS fold (PAS)PAS foldThe PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (M ...The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Domain
L [auth N]PF14598PAS domain (PAS_11)PAS domainThis family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6) [1].Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3.1
B, F
Histone H4
C, G
Histone H2A type 1-B/E
D, H
Histone H2B type 1-J
DNA (124-MER)---
DNA (124-MER)---
K [auth M]Circadian locomoter output cycles protein kaput
L [auth N]Basic helix-loop-helix ARNT-like protein 1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Histone H2A/H2B/H3Domain
A, E
IPR000164Histone H3/CENP-AFamily
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR001951Histone H4Family
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
IPR007125Histone H2A/H2B/H3Domain
C, G
IPR002119Histone H2AFamily
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR007125Histone H2A/H2B/H3Domain
D, H
IPR000558Histone H2BFamily
K [auth M]IPR047230Circadian locomoter output cycles protein kaput-likeFamily
K [auth M]IPR001067Nuclear translocatorFamily
K [auth M]IPR035965PAS domain superfamilyHomologous Superfamily
K [auth M]IPR001610PAC motifRepeat
K [auth M]IPR036638Helix-loop-helix DNA-binding domain superfamilyHomologous Superfamily
K [auth M]IPR013767PAS foldDomain
K [auth M]IPR000014PAS domainDomain
K [auth M]IPR011598Myc-type, basic helix-loop-helix (bHLH) domainDomain
L [auth N]IPR001067Nuclear translocatorFamily
L [auth N]IPR035965PAS domain superfamilyHomologous Superfamily
L [auth N]IPR001610PAC motifRepeat
L [auth N]IPR036638Helix-loop-helix DNA-binding domain superfamilyHomologous Superfamily
L [auth N]IPR013767PAS foldDomain
L [auth N]IPR000014PAS domainDomain
L [auth N]IPR011598Myc-type, basic helix-loop-helix (bHLH) domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, E
PharosP68431
B, F
PharosP62805
C, G
PharosP04908
D, H
PharosP06899