8hxy.1 | SWISS-MODEL Template Library

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SMTL ID : 8hxy.1

Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1:	6 residues within 4Å: Chain E: K.18 Chain L: H.150, D.186, H.188, D.274, Y.313 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.186, L:D.186, L:H.188, L:D.274
ZN.2:	4 residues within 4Å: Chain N: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.263, N:C.266, N:H.283, N:C.286
ZN.3:	4 residues within 4Å: Chain N: C.275, C.278, C.303, C.306 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.275, N:C.278, N:C.303, N:C.306
ZN.4:	4 residues within 4Å: Chain N: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.417, N:C.420, N:H.448, N:C.451
ZN.5:	5 residues within 4Å: Chain N: C.440, C.443, T.445, C.466, H.469 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.440, N:C.443, N:C.466, N:H.469

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

Histone H3: AE
Histone H4: BF
Histone H2A: CG
Histone H2B: DH
Transcriptional regulatory protein SIN3: K
Histone deacetylase RPD3: L
Chromatin modification-related protein EAF3: M
Transcriptional regulatory protein RCO1: NO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

K
K

L
L

M
M

N
N

O
P

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3

Histone H4

Histone H2A

Histone H2B

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Transcriptional regulatory protein RCO1

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