8jho.1 | SWISS-MODEL Template Library

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SMTL ID : 8jho.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-1-1-2-2-mer

Ligands

7 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.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.4:	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.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
ZN.6:	5 residues within 4Å: Chain O: R.300 Chain P: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.263, P:C.266, P:H.283, P:C.286
ZN.7:	4 residues within 4Å: Chain P: C.275, C.278, C.303, C.306 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.275, P:C.278, P:C.303, P: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

Histone H3: AEQU
Histone H4: BFRV
Histone H2A: CGSW
Histone H2B: DHTX
Transcriptional regulatory protein SIN3: K
Histone deacetylase RPD3: L
Chromatin modification-related protein EAF3: MO
RCO1 isoform 1: NP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

Q
a

U
e

B
B

F
F

R
b

V
f

C
C

G
G

S
c

W
g

D
D

H
H

T
d

X
h

K
K

L
L

M
M

O
O

N
N

P
P

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Histone H3

Toggle Identical (AQ)

Histone H4

Toggle Identical (FV)

Histone H2A

Toggle Identical (CS) Toggle Identical (GW)

Histone H2B

Toggle Identical (DT) Toggle Identical (HX)

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

RCO1 isoform 1

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