SMTL ID : 9gfb.1

CryoEM structure of the human INO80 core-nucleosome complex state N-7

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: S.17, H.18, H.20, G.38, L.39, V.40, Q.42, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, E.303, N.332, Y.366, I.374, R.404 Chain D: D.349, R.353 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.17, A:S.17, A:H.18, A:V.40, A:G.73, A:T.74, A:G.75, A:K.76, A:T.77, A:A.78, A:E.303, A:N.332, A:Y.366, A:Y.366, D:D.349 Salt bridges: A:H.18, A:K.76, A:K.76, A:R.404, A:R.404, A:R.404, D:R.353

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

ADP.2: 18 residues within 4Å: Chain B: 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, L.403, R.404 Chain E: R.353 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:S.17, B:S.17, B:H.18, B:V.40, B:G.73, B:T.74, B:G.75, B:K.76, B:T.77, B:A.78, B:Y.366, B:Y.366, E:E.317 Salt bridges: B:H.18, B:K.76, B:R.404, B:R.404, E:R.353 ADP.3: 18 residues within 4Å: Chain C: 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, L.403, R.404 Chain F: E.317 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.17, C:V.40, C:V.40, C:P.71, C:G.73, C:T.74, C:T.74, C:G.75, C:K.76, C:T.77, C:T.77, C:A.78, C:Y.366 Salt bridges: C:H.18, C:K.76, C:R.404, C:R.404 ADP.4: 18 residues within 4Å: Chain B: R.357 Chain D: A.24, H.25, H.27, M.46, V.47, P.79, G.80, T.81, G.82, K.83, T.84, A.85, Y.362, I.370, R.374, R.400, I.403 16 PLIP interactions: 1 interactions with chain B, 15 interactions with chain D Hydrogen bonds: B:R.357, D:A.24, D:V.47, D:V.47, D:G.80, D:T.81, D:G.82, D:K.83, D:T.84, D:A.85, D:N.329, D:Y.362 Salt bridges: D:H.25, D:K.83, D:R.400, D:R.400 ADP.5: 17 residues within 4Å: Chain E: 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, I.370, L.399, R.400 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:A.24, E:V.47, E:G.80, E:T.81, E:G.82, E:K.83, E:T.84, E:A.85, E:Y.362, E:Y.362 Salt bridges: E:H.25, E:K.83, E:R.400, E:R.400 ADP.6: 21 residues within 4Å: Chain A: R.357 Chain F: A.24, H.25, H.27, G.45, M.46, V.47, Q.49, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, I.370, L.399, R.400, I.403 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:H.25, F:V.47, F:G.80, F:T.81, F:G.82, F:K.83, F:T.84, F:A.85, F:N.329, F:Y.362, F:Y.362, A:R.357 Salt bridges: F:H.25, F:K.83, F:R.400, F:R.400, A:R.357 ADP.7: 12 residues within 4Å: Chain G: Q.522, E.544, M.545, G.546, L.547, G.548, K.549, T.550, V.551, N.1184, R.1209, R.1212 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:L.518, G:Q.522, G:G.546, G:L.547, G:G.548, G:K.549, G:T.550, G:N.1184, G:R.1209 Salt bridges: G:K.549, G:R.1212, G:R.1212

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain H: C.309, S.310, V.311, P.312 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.309, H:S.310, H:V.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, M. et al., CryoEM structure of the human INO80 core-nucleosome complex state N-7. To Be Published

Release Date

2025-08-20

Peptides

RuvB-like 1: ABC
RuvB-like 2: DEF
Chromatin-remodeling ATPase INO80: G
INO80 complex subunit B: H
INO80 complex subunit C: I
Actin-related protein 5: J
Histone H3.1: MQ
Histone H4: NR
Histone H2A type 1-B/E: OS
Histone H2B type 2-E: PT

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

M
M

Q
Q

N
N

R
R

O
O

S
S

P
P

T
T

RuvB-like 1

RuvB-like 2

Chromatin-remodeling ATPase INO80

INO80 complex subunit B

INO80 complex subunit C

Actin-related protein 5

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 2-E

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