SMTL ID : 8hpo.1

Cryo-EM structure of a SIN3/HDAC complex from budding yeast

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x TPO: PHOSPHOTHREONINE(Non-functional Binders)

TPO.1: 6 residues within 4Å: Chain C: Q.263, P.264, S.265, N.392, H.393 Chain I: E.202 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.264, C:N.392

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain C: D.186, H.188, D.274 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.186, C:H.188, C:D.274 ZN.5: 3 residues within 4Å: Chain D: D.186, H.188, D.274 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.186, D:H.188, D:D.274

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain C: D.184, I.185, D.186, H.188, F.208 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.184, C:D.184, C:H.188 K.4: 4 residues within 4Å: Chain C: F.197, 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 K.6: 6 residues within 4Å: Chain D: D.184, I.185, D.186, H.188, S.207, F.208 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.184, D:D.186, D:H.188, D:S.207 K.7: 6 residues within 4Å: Chain D: F.197, T.200, V.203, M.204, T.205, Y.232 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:V.203, D:T.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Z. et al., Structure of a SIN3-HDAC complex from budding yeast. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-05-03

Peptides

Transcriptional regulatory protein UME1: A
Transcriptional regulatory protein SDS3: B
Histone deacetylase RPD3: CD
Transcriptional regulatory protein SAP30: E
Transcriptional regulatory protein SIN3: FJ
Transcriptional regulatory protein DEP1: G
Transcriptional regulatory protein PHO23: H
Transcriptional regulatory protein RXT2: I
Transcriptional regulatory protein RXT3: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
D

C
F

D
G

E
I

F
A

J
B

G
H

H
C

I
E

K
J

Transcriptional regulatory protein UME1

Transcriptional regulatory protein SDS3

Histone deacetylase RPD3

Transcriptional regulatory protein SAP30

Transcriptional regulatory protein SIN3

Transcriptional regulatory protein DEP1

Transcriptional regulatory protein PHO23

Transcriptional regulatory protein RXT2

Transcriptional regulatory protein RXT3

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