SMTL ID : 8ihn.1

Cryo-EM structure of the Rpd3S core complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain C: D.186, H.188, D.274 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.186, C:D.186, C:H.188, C:D.274

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain C: F.197, Y.198, T.200, V.203, Y.232 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:F.197, C:V.203, C:Y.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Cell Res. (2023)

Release Date

2024-03-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
L

D
M

F
O

E
N

G
P

Histone H3

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

RCO1 isoform 1

Chromatin modification-related protein EAF3

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