8KD5

Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth O]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
G [auth S]SCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
D [auth P]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
H [auth T]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
E [auth Q]SCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
I [auth U]SCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
F [auth R]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
J [auth V]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
O [auth E],
P [auth G]
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
D [auth P],
H [auth T]
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
E [auth Q],
I [auth U]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
M [auth A]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
N [auth B]PF08295Sin3 family co-repressor (Sin3_corepress)Sin3 family co-repressorThis domain is found on transcriptional regulators. It forms interactions with histone deacetylases [1].Domain
N [auth B]PF02671Paired amphipathic helix repeat (PAH)Paired amphipathic helix repeat- Repeat
N [auth B]PF16879C-terminal domain of Sin3a protein (Sin3a_C)C-terminal domain of Sin3a protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth D],
B [auth F]
Chromatin modification-related protein EAF3
O [auth E],
P [auth G]
Transcriptional regulatory protein RCO1
C [auth O],
G [auth S]
Histone H3 -
D [auth P],
H [auth T]
Histone H4
E [auth Q],
I [auth U]
Histone H2A -
F [auth R],
J [auth V]
Histone H2B 1.1 -
K [auth X]187bp DNA---
L [auth Y]187bp DNA---
M [auth A]Histone deacetylase RPD3
N [auth B]Transcriptional regulatory protein SIN3

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth D],
B [auth F]
IPR016197Chromo-like domain superfamilyHomologous Superfamily
A [auth D],
B [auth F]
IPR008676MRGFamily
A [auth D],
B [auth F]
IPR038217MRG, C-terminal domain superfamilyHomologous Superfamily
A [auth D],
B [auth F]
IPR000953Chromo/chromo shadow domainDomain
A [auth D],
B [auth F]
IPR053820MSL3 chromodomain-likeDomain
A [auth D],
B [auth F]
IPR026541MRG domainDomain
O [auth E],
P [auth G]
IPR001965Zinc finger, PHD-typeDomain
O [auth E],
P [auth G]
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
O [auth E],
P [auth G]
IPR052819Chromatin-associated regulatory proteinFamily
O [auth E],
P [auth G]
IPR019787Zinc finger, PHD-fingerDomain
O [auth E],
P [auth G]
IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
O [auth E],
P [auth G]
IPR019786Zinc finger, PHD-type, conserved siteConserved Site
C [auth O],
G [auth S]
IPR009072Histone-foldHomologous Superfamily
C [auth O],
G [auth S]
IPR007125Histone H2A/H2B/H3Domain
C [auth O],
G [auth S]
IPR000164Histone H3/CENP-AFamily
D [auth P],
H [auth T]
IPR009072Histone-foldHomologous Superfamily
D [auth P],
H [auth T]
IPR001951Histone H4Family
D [auth P],
H [auth T]
IPR035425CENP-T/Histone H4, histone foldDomain
D [auth P],
H [auth T]
IPR019809Histone H4, conserved siteConserved Site
D [auth P],
H [auth T]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
E [auth Q],
I [auth U]
IPR009072Histone-foldHomologous Superfamily
E [auth Q],
I [auth U]
IPR007125Histone H2A/H2B/H3Domain
E [auth Q],
I [auth U]
IPR002119Histone H2AFamily
E [auth Q],
I [auth U]
IPR032454Histone H2A, C-terminal domainDomain
E [auth Q],
I [auth U]
IPR032458Histone H2A conserved siteConserved Site
F [auth R],
J [auth V]
IPR009072Histone-foldHomologous Superfamily
F [auth R],
J [auth V]
IPR007125Histone H2A/H2B/H3Domain
F [auth R],
J [auth V]
IPR000558Histone H2BFamily
M [auth A]IPR000286Histone deacetylase familyFamily
M [auth A]IPR023801Histone deacetylase domainDomain
M [auth A]IPR003084Histone deacetylaseFamily
M [auth A]IPR037138Histone deacetylase domain superfamilyHomologous Superfamily
M [auth A]IPR023696Ureohydrolase domain superfamilyHomologous Superfamily
M [auth A]IPR050284Histone deacetylase and polyamine deacetylaseFamily
N [auth B]IPR039774Transcriptional regulatory protein Sin3-likeFamily
N [auth B]IPR013194Histone deacetylase interacting domainDomain
N [auth B]IPR003822Paired amphipathic helixRepeat
N [auth B]IPR036600Paired amphipathic helix superfamilyHomologous Superfamily
N [auth B]IPR031693Sin3, C-terminalDomain

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
C [auth O],
G [auth S]
M3L Parent Component: LYS

RESIDAA0074

PSI-MOD :  N6,N6,N6-trimethyl-L-lysine MOD:00083