SMTL ID : 7yi2.1

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

Coordinates

PDB Format Compare

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 D: D.186, H.188, D.274 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.186, D:D.186, D:H.188, D:D.274 ZN.2: 4 residues within 4Å: 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.3: 6 residues within 4Å: Chain F: C.275, T.277, C.278, H.302, C.303, C.306 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.278, F:C.306 ZN.4: 4 residues within 4Å: Chain F: C.440, C.443, C.466, H.469 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.440, F:C.443, F:C.466, F:H.469 ZN.5: 4 residues within 4Å: Chain F: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.417, F:C.420, F:H.448, F:C.451

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: C
Histone deacetylase RPD3: D
Chromatin modification-related protein EAF3: E
Transcriptional regulatory protein RCO1: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Transcriptional regulatory protein RCO1

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