SMTL ID : 8w9c.1

Cryo-EM structure of the Rpd3S complex from budding yeast

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-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: 4 residues within 4Å: Chain B: C.275, 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: 3 residues within 4Å: Chain B: C.440, C.443, C.466 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 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.420, B:H.448, B:C.451 ZN.5: 3 residues within 4Å: Chain C: D.186, H.188, D.274 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.186, C:D.186, C:H.188, C:D.274 ZN.8: 5 residues within 4Å: Chain E: R.303 Chain F: C.263, C.266, H.283, C.286 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.283, F:C.286 ZN.9: 6 residues within 4Å: Chain F: C.275, C.278, H.302, C.303, E.305, C.306 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.275, F:C.306

2 x K: POTASSIUM ION(Non-covalent)

K.6: 6 residues within 4Å: Chain C: D.184, D.186, H.188, S.207, F.208, H.209 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.184, C:D.186, C:H.188, C:S.207 K.7: 4 residues within 4Å: Chain C: F.197, T.200, V.203, Y.232 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:F.197, C:T.200, C:V.203, C:Y.232

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: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

F
F

C
B

D
C

E
D

Transcriptional regulatory protein SIN3

Transcriptional regulatory protein RCO1

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

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