SMTL ID : 7zi4.1

Cryo-EM structure of the human INO80 complex bound to a WT nucleosome

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-2-1-1-1-2-2-2-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: S.17, H.18, H.20, G.38, L.39, V.40, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.404 Chain B: E.317, R.353 15 PLIP interactions: 1 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:R.353, A:S.17, A:S.17, A:V.40, A:G.73, A:T.74, A:G.75, A:K.76, A:T.77, A:A.78, A:Y.366, A:Y.366 Salt bridges: A:H.18, A:K.76, A:R.404 ADP.2: 17 residues within 4Å: Chain B: A.24, H.25, H.27, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, R.374, R.400 Chain C: E.320 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.24, B:V.47, B:V.47, B:Q.78, B:G.80, B:T.81, B:G.82, B:K.83, B:T.84, B:T.84, B:T.84, B:A.85 Salt bridges: B:H.25, B:K.83, B:R.400, B:R.400 ADP.3: 17 residues within 4Å: Chain C: S.17, H.18, H.20, G.38, L.39, V.40, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, R.404 Chain D: E.317 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.17, C:S.17, C:H.18, C:V.40, C:G.73, C:T.74, C:T.74, C:G.75, C:K.76, C:T.77, C:A.78, C:Y.366, D:E.317 Salt bridges: C:H.18, C:K.76, C:R.404, C:R.404 ADP.4: 16 residues within 4Å: Chain D: A.24, H.25, H.27, G.45, M.46, V.47, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, L.399, R.400 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:A.24, D:V.47, D:G.80, D:T.81, D:T.81, D:G.82, D:K.83, D:T.84, D:A.85, D:Y.362, D:Y.362 Salt bridges: D:H.25, D:K.83, D:R.400, D:R.400 ADP.5: 19 residues within 4Å: Chain E: S.17, H.18, H.20, G.38, L.39, V.40, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, L.403, R.404 Chain F: R.353 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.17, E:S.17, E:V.40, E:G.73, E:T.74, E:G.75, E:K.76, E:T.77, E:T.77, E:A.78, E:Y.366, E:Y.366, F:R.353 Salt bridges: E:H.18, E:K.76, E:R.404, E:R.404 ADP.6: 19 residues within 4Å: Chain F: A.24, H.25, H.27, G.45, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:A.24, F:V.47, F:G.80, F:T.81, F:G.82, F:K.83, F:T.84, F:A.85, F:Y.362, F:Y.362 Salt bridges: F:H.25, F:K.83, F:R.400 ADP.7: 12 residues within 4Å: Chain G: E.544, M.545, G.546, L.547, G.548, K.549, T.550, V.551, N.1184, R.1212, L.1213 Ligands: BEF.8 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.546, G:L.547, G:G.548, G:K.549, G:T.550, G:R.1212 Salt bridges: G:K.549, G:K.549, G:R.1212 ADP.10: 16 residues within 4Å: Chain J: G.38, S.39, F.40, R.43, D.166, G.189, Y.190, G.215, S.216, E.243, H.247, G.496, N.497, M.499, Y.500, V.530 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:N.37, J:S.39, J:F.40, J:R.43, J:R.43, J:N.101, J:Y.190, J:E.243 Salt bridges: J:R.43 pi-Cation interactions: J:H.247, J:H.247

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.8: 6 residues within 4Å: Chain G: M.545, E.653, G.1182, N.1184, R.1212 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain I: C.309, C.314, C.330, C.334 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.309, I:C.314, I:C.330, I:C.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vance, N.R. et al., Cryo-EM structure of the human INO80 complex bound to a WT nucleosome. To Be Published

Release Date

2023-04-19

Peptides

RuvB-like 1: ACE
RuvB-like 2: BDF
Chromatin-remodeling ATPase INO80: G
Histone H4: HM
INO80 complex subunit B: I
Actin-related protein 5: J
INO80 complex subunit C: K
Histone H3.1: LP
Histone H2A type 1-B/E: NQ
Histone H2B type 1-J: OR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
N

M
J

I
R

J
H

K
Q

L
I

P
M

N
K

Q
O

O
L

R
P

RuvB-like 1

RuvB-like 2

Chromatin-remodeling ATPase INO80

Histone H4

INO80 complex subunit B

Actin-related protein 5

INO80 complex subunit C

Histone H3.1

Histone H2A type 1-B/E

Histone H2B type 1-J

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