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SMTL ID : 8hy0.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-1-1-2-2-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.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
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: AE
Histone H4: BF
Histone H2A: CG
Histone H2B: DH
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

B
B

F
F

C
C

G
G

D
D

H
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

Histone H4

Histone H2A

Histone H2B

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

RCO1 isoform 1

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1kx3.1 | 1kx4.1 | 1kx5.1 | 1m18.1 | 1m19.1 | 1m1a.1 | 1p34.1 | 1p3a.1 | 1p3k.1 | 1p3l.1 | 1p3m.1 | 1s32.1 | 1zbb.1 | 1zla.1 | 2fj7.1 | 2io5.1 | 2nzd.1 | 3b6f.1 | 3b6g.1 | 3c1b.1 | 3c1c.1 | 3c9k.1 | 3c9k.2 | 3kuy.1 | 3kxb.1 | 3lel.1 | 3lel.2 | 3lja.1 | 3lz0.1 | 3lz1.1 more...less...

3mgp.1 | 3mgq.1 | 3mgr.1 | 3mgs.1 | 3mnn.1 | 3mvd.1 | 3o62.1 | 3reh.1 | 3rei.1 | 3rej.1 | 3rek.1 | 3rel.1 | 3tu4.1 | 3tu4.2 | 3ut9.1 | 3uta.1 | 3utb.1 | 3x1s.1 | 3x1t.1 | 3x1u.1 | 3x1v.1 | 4h9n.1 | 4h9o.1 | 4h9p.1 | 4h9p.2 | 4h9q.1 | 4h9q.2 | 4h9r.1 | 4h9r.2 | 4j8u.1 | 4j8v.1 | 4j8v.2 | 4j8v.3 | 4j8w.1 | 4j8x.1 | 4j8x.2 | 4j8x.3 | 4r8p.1 | 4wu8.1 | 4wu9.1 | 4xuj.1 | 5bnv.1 | 5bnx.1 | 5bo0.1 | 5bs7.1 | 5bsa.1 | 5cp6.1 | 5dnm.1 | 5dnn.1 | 5f99.1 | 5gsu.1 | 5gt0.1 | 5gt3.1 | 5hq2.1 | 5ja4.1 | 5kdm.1 | 5nl0.1 | 5nl0.2 | 5omx.1 | 5ong.1 | 5onw.1 | 5oxv.1 | 5oy7.1 | 5x0y.1 | 5xf6.1 | 5z3l.1 | 5z3o.1 | 5z3u.1 | 5z3v.1 | 6esf.1 | 6esg.1 | 6esh.1 | 6esi.1 | 6fml.1 | 6iro.1 | 6jyl.1 | 6k1p.1 | 6kiu.1 | 6kiv.1 | 6kiw.1 | 6kix.1 | 6kiz.1 | 6nj9.1 | 6nn6.1 | 6nog.1 | 6nqa.1 | 6pa7.1 | 6pwv.1 | 6pww.1 | 6pwx.1 | 6r1u.1 | 6r25.1 | 6s01.1 | 6t9l.1 | 6tda.1 | 6tem.1 | 6ugm.1 | 6uh5.1 | 6uxw.1 | 6ven.1 | 6vyp.1 | 6vyp.2 | 6w5i.1 | 6w5m.1 | 6w5n.1 | 6wz5.1 | 6wz9.1 | 6x0n.1 | 6x59.1 | 6x5a.1 | 6xjd.1 | 7a08.1 | 7at8.1 | 7bwd.1 | 7ciz.1 | 7ciz.2 | 7ciz.3 | 7cj0.1 | 7cj0.2 | 7cro.1 | 7crp.1 | 7crq.1 | 7crr.1 | 7e8d.1 | 7e8i.1 | 7eg6.1 | 7egp.1 | 7enn.1 | 7jzv.1 | 7mbm.1 | 7mbn.1 | 7oh9.1 | 7oha.1 | 7ohb.1 | 7ohc.1 | 7swy.1 | 7tn2.1 | 7u50.1 | 7u51.1 | 7u52.1 | 7u53.1 | 7uv9.1 | 7v1m.1 | 7v1m.2 | 7xpx.1 | 7y8r.1 | 7yi0.1 | 7yi1.1 | 7yi2.1 | 7yi3.1 | 7yi4.1 | 7yi5.1 | 7zs9.1 | 7zsa.1 | 7zsb.1 | 8aag.1 | 8atf.1 | 8av6.1 | 8cbn.1 | 8cbq.1 | 8ceo.1 | 8cww.1 | 8cze.1 | 8f86.1 | 8g86.1 | 8g88.1 | 8g8b.1 | 8g8g.1 | 8ga8.1 | 8gui.1 | 8guj.1 | 8guk.1 | 8hag.1 | 8hah.1 | 8hai.1 | 8haj.1 | 8hak.1 | 8hal.1 | 8ham.1 | 8han.1 | 8hpo.1 | 8hxx.1 | 8hxy.1 | 8hxz.1 | 8ihm.1 | 8ihn.1 | 8iht.1 | 8jbx.1 | 8jcc.1 | 8jcd.1 | 8jho.1 | 8kc7.1 | 8kd2.1 | 8kd3.1 | 8kd4.1 | 8kd5.1 | 8kd6.1 | 8kd7.1 | 8oo7.1 | 8ooa.1 | 8oop.1 | 8oos.1 | 8pc5.1 | 8pc6.1 | 8peo.1 | 8pep.1 | 8qzm.1 | 8siy.1 | 8t3t.1 | 8t3w.1 | 8t3y.1 | 8tof.1 | 8uxq.1 | 8v4y.1 | 8v6v.1 | 8v7l.1 | 8vws.1 | 8vwt.1 | 8vwu.1 | 8vwv.1 | 8w9c.1 | 8w9d.1 | 8w9e.1 | 8w9f.1 | 8yv8.1 | 9ipu.1

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Background

Transparent

Resolution

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