SMTL ID : 8hxx.1

Cryo-EM structure of the histone deacetylase complex Rpd3S

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: H.150, D.186, H.188, D.274, Y.313 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:D.186, B:H.188, B:D.274 ZN.2: 4 residues within 4Å: Chain D: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.263, D:C.266, D:H.283, D:C.286 ZN.3: 4 residues within 4Å: Chain D: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.417, D:C.420, D:H.448, D:C.451 ZN.4: 4 residues within 4Å: Chain D: C.275, C.278, C.303, C.306 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.275, D:C.278, D:C.303, D:C.306 ZN.5: 4 residues within 4Å: Chain D: C.440, C.443, C.466, H.469 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.440, D:C.443, D:C.466, D:H.469 ZN.6: 5 residues within 4Å: Chain E: R.300 Chain F: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.263, F:C.266, F:H.283, F:C.286 ZN.7: 4 residues within 4Å: Chain F: C.275, C.278, C.303, C.306 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.275, F:C.278, F:C.303, F:C.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Structure of histone deacetylase complex Rpd3S bound to nucleosome. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-09-27

Peptides

Transcriptional regulatory protein SIN3: A
Histone deacetylase RPD3: B
Chromatin modification-related protein EAF3: CE
RCO1 isoform 1: DF
Histone H3: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

E
O

D
N

F
P

G
E

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

RCO1 isoform 1

Histone H3

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