SMTL ID : 7yi3.1

Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain B: D.186, H.188, D.274 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.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.3: 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.4: 4 residues within 4Å: Chain D: C.275, C.278, C.303, C.306 2 PLIP interactions: 2 interactions with chain D Metal complexes: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, H. et al., Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S. Nature (2023)

Release Date

2023-06-14

Peptides

Transcriptional regulatory protein SIN3: A
Histone deacetylase RPD3: B
Chromatin modification-related protein EAF3: C
Transcriptional regulatory protein RCO1: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Transcriptional regulatory protein RCO1

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