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SMTL ID : 8w9e.1

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-3-2-2-2-2-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1:	5 residues within 4Å: Chain B: C.263, C.266, H.283, C.286 Chain D: R.300 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.263, B:C.266, B:H.283, B:C.286
ZN.2:	5 residues within 4Å: Chain B: C.275, T.277, C.278, C.303, C.306 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.275, B:C.278, B:C.303, B:C.306
ZN.3:	4 residues within 4Å: Chain B: C.440, C.443, C.466, H.469 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.440, B:C.443, B:C.466
ZN.4:	4 residues within 4Å: Chain B: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.417, B:C.420, B:H.448, B:C.451
ZN.5:	4 residues within 4Å: Chain C: D.186, H.188, D.274, Y.313 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.186, C:H.188, C:D.274
ZN.7:	4 residues within 4Å: Chain F: C.263, C.266, H.283, C.286 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.263, F:H.283, F:C.286
ZN.8:	5 residues within 4Å: Chain F: C.275, C.278, F.282, H.302, C.303 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.303

1 x K: POTASSIUM ION(Non-covalent)

K.6:	5 residues within 4Å: Chain C: F.197, Y.198, T.200, V.203, Y.232 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:F.197, C:T.200

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wang, C. et al., Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv (2024)

Release Date

2024-05-15

Peptides

Transcriptional regulatory protein SIN3: A
Transcriptional regulatory protein RCO1: BF
Histone deacetylase RPD3: C
Chromatin modification-related protein EAF3: DEQ
Histone H3.1: GK
Histone H4: HL
Histone H2A type 1-B/E: IM
Histone H2B type 1-K: JN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

F
F

C
B

D
C

E
D

Q
G

G
a

K
e

H
b

L
f

I
c

M
g

J
d

N
h

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Transcriptional regulatory protein SIN3

Transcriptional regulatory protein RCO1

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-K

Toggle Identical (JN)

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