SMTL ID : 7uqj.1

Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: D.451, I.452, G.453, P.492, P.493, G.494, T.495, G.496, K.497, T.498, L.499, R.502, I.631, Q.635, G.660, A.661, R.664 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.453, A:G.453, A:G.494, A:T.495, A:G.496, A:K.497, A:T.498, A:T.498, A:T.498, A:L.499, A:R.502, A:Q.635, A:G.660, A:A.661 Salt bridges: A:K.497

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 20 residues within 4Å: Chain A: D.584, M.586, R.613 Chain B: D.451, I.452, G.453, L.455, P.493, G.494, T.495, G.496, K.497, T.498, L.499, R.502, D.555, I.631, G.660, A.661, R.664 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.453, B:G.453, B:G.494, B:T.495, B:G.496, B:K.497, B:T.498, B:T.498, B:L.499, B:R.502, B:R.664, A:R.613, A:R.613 Salt bridges: B:K.497 AGS.3: 23 residues within 4Å: Chain B: D.584, A.607, R.610, R.613 Chain C: D.451, I.452, G.453, L.455, P.493, G.494, T.495, G.496, K.497, T.498, L.499, R.502, E.556, I.631, Q.635, G.660, A.661, R.664 Ligands: MG.4 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.453, C:G.494, C:T.495, C:T.495, C:G.496, C:K.497, C:K.497, C:T.498, C:L.499, C:R.502, C:Q.635, C:R.664, B:R.610, B:R.613 Salt bridges: C:K.497, B:R.610, B:R.610 AGS.5: 22 residues within 4Å: Chain C: A.607, R.610, R.613 Chain D: D.451, I.452, G.453, L.455, P.493, G.494, T.495, G.496, K.497, T.498, L.499, R.502, E.556, I.631, Q.635, G.660, A.661, R.664 Ligands: MG.6 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.453, D:G.453, D:G.494, D:T.495, D:T.495, D:G.496, D:K.497, D:K.497, D:T.498, D:L.499, D:R.502, D:Q.635, D:R.664, D:R.664, C:R.610, C:R.613 Salt bridges: D:K.497, C:R.610, C:R.610 AGS.7: 22 residues within 4Å: Chain D: D.584, R.610, R.613 Chain E: D.451, I.452, G.453, L.455, P.493, G.494, T.495, G.496, K.497, T.498, L.499, R.502, N.599, I.631, Q.635, G.660, A.661, R.664 Ligands: MG.8 22 PLIP interactions: 17 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:G.453, E:G.494, E:T.495, E:T.495, E:T.495, E:G.496, E:K.497, E:K.497, E:T.498, E:T.498, E:L.499, E:R.502, E:N.599, E:Q.635, E:G.660, E:R.664, D:R.610, D:R.613, D:R.613 Salt bridges: E:K.497, D:R.610, D:R.610 AGS.9: 20 residues within 4Å: Chain E: R.610, R.613 Chain F: D.451, I.452, G.453, P.493, G.494, T.495, G.496, K.497, T.498, L.499, E.556, N.599, I.631, Q.635, G.660, A.661, R.664 Ligands: MG.10 19 PLIP interactions: 16 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:G.453, F:G.453, F:G.494, F:T.495, F:T.495, F:G.496, F:K.497, F:K.497, F:T.498, F:T.498, F:L.499, F:N.599, F:Q.635, F:G.660, F:R.664, E:R.613 Salt bridges: F:K.497, E:R.610, E:R.610

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: D.584, R.610 Chain C: T.498 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.498 MG.6: 4 residues within 4Å: Chain D: T.498, D.555, E.556 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.498 MG.8: 4 residues within 4Å: Chain D: D.584 Chain E: T.498, E.556 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.498 MG.10: 4 residues within 4Å: Chain F: T.498, D.555, E.556 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.498

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly. J.Biol.Chem. (2022)

Release Date

2023-02-01

Peptides

ATPase histone chaperone YTA7: ABCDEF
Histone H3: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATPase histone chaperone YTA7

Histone H3

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