SMTL ID : 8ooc.1

CryoEM Structure INO80core Hexasome complex Rvb core refinement state1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-1-1-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: A.18, H.19, H.21, G.39, F.40, V.41, G.72, P.73, G.74, T.75, G.76, K.77, T.78, A.79, Y.367, I.375, R.405, L.408 Chain D: R.313, E.316, R.352 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.19, A:V.41, A:G.74, A:T.75, A:G.76, A:K.77, A:T.78, A:T.78, A:A.79, A:Y.367, A:Y.367, D:R.352 Salt bridges: A:H.19, A:K.77, A:R.405, A:R.405, D:R.313, D:R.313 ADP.2: 21 residues within 4Å: Chain B: A.18, H.19, H.21, G.39, F.40, V.41, Q.43, G.72, P.73, G.74, T.75, G.76, K.77, T.78, A.79, Y.367, I.375, L.404, R.405 Chain E: R.313, E.316 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:A.18, B:V.41, B:V.41, B:G.74, B:T.75, B:G.76, B:K.77, B:T.78, B:T.78, B:A.79, B:Y.367, E:R.313, E:E.316 Salt bridges: B:H.19, B:K.77, B:R.405, B:R.405, E:R.313 ADP.3: 20 residues within 4Å: Chain C: A.18, H.19, H.21, I.22, G.39, F.40, V.41, Q.43, G.72, P.73, G.74, T.75, G.76, K.77, T.78, A.79, Y.367, L.404, R.405, L.408 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:H.19, C:V.41, C:G.74, C:T.75, C:G.76, C:K.77, C:T.78, C:T.78, C:A.79, C:Y.367, C:Y.367 Salt bridges: C:H.19, C:K.77, C:R.405, C:R.405 ADP.4: 17 residues within 4Å: Chain D: A.23, H.24, H.26, I.27, G.45, L.46, V.47, P.79, S.80, G.82, K.83, T.84, A.85, Y.361, I.369, L.398, R.399 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:H.24, D:V.47, D:S.80, D:G.82, D:K.83, D:T.84, D:T.84, D:A.85, D:Y.361, D:Y.361 Salt bridges: D:H.24, D:K.83, D:R.399, D:R.399 ADP.5: 18 residues within 4Å: Chain E: A.23, H.24, H.26, G.45, L.46, V.47, Q.49, P.78, S.80, T.81, G.82, K.83, T.84, A.85, Y.361, I.369, L.398, R.399 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:H.24, E:V.47, E:S.80, E:T.81, E:G.82, E:K.83, E:T.84, E:T.84, E:A.85, E:Y.361, E:Y.361 Salt bridges: E:H.24, E:K.83, E:R.399, E:R.399 ADP.6: 17 residues within 4Å: Chain F: A.23, H.24, H.26, G.45, L.46, V.47, P.79, S.80, T.81, G.82, K.83, T.84, A.85, Y.361, I.369, L.398, R.399 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:H.24, F:V.47, F:S.80, F:T.81, F:G.82, F:K.83, F:T.84, F:T.84, F:A.85, F:Y.361, F:Y.361 Salt bridges: F:H.24, F:K.83, F:R.399, F:R.399

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain J: R.69, D.190 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.190

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.8: 20 residues within 4Å: Chain J: N.63, G.64, S.65, H.66, S.67, R.69, D.190, S.209, Y.210, S.211, G.235, E.264, R.268, G.690, G.691, N.692, L.694, F.695, I.725 Ligands: MG.7 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.64, J:S.65, J:H.66, J:S.67, J:S.209, J:Y.210, J:S.211, J:S.211, J:R.268, J:G.691 Salt bridges: J:R.69, J:R.69 pi-Stacking: J:F.695 pi-Cation interactions: J:R.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, M. et al., Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Science (2023)

Release Date

2023-08-02

Peptides

RuvB-like helicase: ABC
RuvB-like helicase: DEF
Chromatin-remodeling ATPase Ino80: G
INO80 complex subunit B-like conserved region domain-containing protein: H
Vps72/YL1 C-terminal domain-containing protein: I
DASH complex subunit DAD4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

RuvB-like helicase

RuvB-like helicase

Chromatin-remodeling ATPase Ino80

INO80 complex subunit B-like conserved region domain-containing protein

Vps72/YL1 C-terminal domain-containing protein

DASH complex subunit DAD4

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