8HXX

Cryo-EM structure of the histone deacetylase complex Rpd3S


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
B [auth L]PF00850e8hxxL1 A: a/b three-layered sandwichesX: HAD domain-likeH: HAD domain-relatedT: Arginase/deacetylaseF: PF00850ECOD (1.6)
C [auth M]PF05712e8hxxM1 A: alpha arraysX: MRG domain (From Topology)H: MRG domain (From Topology)T: MRG domainF: PF05712ECOD (1.6)
E [auth O]PF05712e8hxxO1 A: alpha arraysX: MRG domain (From Topology)H: MRG domain (From Topology)T: MRG domainF: PF05712ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth K]PF08295Sin3 family co-repressor (Sin3_corepress)Sin3 family co-repressorThis domain is found on transcriptional regulators. It forms interactions with histone deacetylases [1].Domain
A [auth K]PF02671Paired amphipathic helix repeat (PAH)Paired amphipathic helix repeat- Repeat
A [auth K]PF16879C-terminal domain of Sin3a protein (Sin3a_C)C-terminal domain of Sin3a protein- Family
B [auth L]PF00850Histone deacetylase domain (Hist_deacetyl)Histone deacetylase domainHistones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].
Domain
D [auth N],
F [auth P]
PF00628PHD-finger (PHD)PHD-fingerPHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].Domain
G [auth E]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth K]Transcriptional regulatory protein SIN3
B [auth L]Histone deacetylase RPD3
C [auth M],
E [auth O]
Chromatin modification-related protein EAF3-
D [auth N],
F [auth P]
RCO1 isoform 1
G [auth E]Histone H3 -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth K]IPR039774Transcriptional regulatory protein Sin3-likeFamily
A [auth K]IPR013194Histone deacetylase interacting domainDomain
A [auth K]IPR003822Paired amphipathic helixRepeat
A [auth K]IPR036600Paired amphipathic helix superfamilyHomologous Superfamily
A [auth K]IPR031693Sin3, C-terminalDomain
B [auth L]IPR000286Histone deacetylase familyFamily
B [auth L]IPR023801Histone deacetylase domainDomain
B [auth L]IPR003084Histone deacetylaseFamily
B [auth L]IPR037138Histone deacetylase domain superfamilyHomologous Superfamily
B [auth L]IPR023696Ureohydrolase domain superfamilyHomologous Superfamily
C [auth M],
E [auth O]
IPR000953Chromo/chromo shadow domainDomain
C [auth M],
E [auth O]
IPR016197Chromo-like domain superfamilyHomologous Superfamily
C [auth M],
E [auth O]
IPR025995RNA binding activity-knot of a chromodomainDomain
C [auth M],
E [auth O]
IPR008676MRGFamily
C [auth M],
E [auth O]
IPR026541MRG domainDomain
C [auth M],
E [auth O]
IPR038217MRG, C-terminal domain superfamilyHomologous Superfamily
D [auth N],
F [auth P]
IPR001965Zinc finger, PHD-typeDomain
D [auth N],
F [auth P]
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
D [auth N],
F [auth P]
IPR019787Zinc finger, PHD-fingerDomain
D [auth N],
F [auth P]
IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
D [auth N],
F [auth P]
IPR019786Zinc finger, PHD-type, conserved siteConserved Site
G [auth E]IPR009072Histone-foldHomologous Superfamily
G [auth E]IPR007125Histone H2A/H2B/H3Domain
G [auth E]IPR000164Histone H3/CENP-AFamily