SMTL ID : 8c60.1

Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: D.177, I.178, H.179, D.265 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.177, B:H.179, B:H.179, B:D.265 ZN.4: 4 residues within 4Å: Chain C: C.289, C.292, C.315, H.318 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.289, C:C.292, C:C.315, C:H.318 ZN.5: 4 residues within 4Å: Chain C: C.274, C.277, H.297, C.300 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.274, C:C.277, C:H.297, C:C.300 ZN.6: 4 residues within 4Å: Chain C: C.71, C.74, C.99, C.102 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.71, C:C.74, C:C.99, C:C.102 ZN.7: 5 residues within 4Å: Chain C: C.59, S.61, C.62, H.79, C.82 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.59, C:S.61, C:C.62, C:H.79, C:C.82

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain B: D.175, D.177, H.179, H.180, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.175, B:D.177, B:H.179, B:S.198, B:F.199 CA.3: 4 residues within 4Å: Chain B: F.188, T.191, V.194, Y.223 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:F.188, B:V.194, B:Y.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, M.S.M. et al., Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Nat Commun (2023)

Release Date

2023-05-10

Peptides

Isoform 2 of Paired amphipathic helix protein Sin3b: A
Histone deacetylase 2: B
PHD finger protein 12: C
Mortality factor 4-like protein 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoform 2 of Paired amphipathic helix protein Sin3b

Histone deacetylase 2

PHD finger protein 12

Mortality factor 4-like protein 1

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