SMTL ID : 9gev.1

CryoEM structure of the human INO80 core-nucleosome complex state N-6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.47 Å

Oligo State

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

Ligands

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

ADP.1: 17 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, L.403, R.404 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.17, A:V.40, A:V.40, A:G.73, A:T.74, A:T.74, A:G.75, A:K.76, A:T.77, A:T.77, A:A.78, A:Y.366 Salt bridges: A:H.18, A:K.76, A:R.404, A:R.404 ADP.2: 19 residues within 4Å: Chain B: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.49, 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 B Hydrogen bonds: B:A.24, B:V.47, B:G.80, B:T.81, B:G.82, B:K.83, B:T.84, B:A.85, B:Y.362, B:Y.362 Salt bridges: B:H.25, B:K.83, B:R.400, B:R.400 ADP.4: 18 residues within 4Å: Chain O: 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, Y.366, L.403, R.404 16 PLIP interactions: 15 interactions with chain O, 1 interactions with chain B Hydrogen bonds: O:S.17, O:H.18, O:V.40, O:V.40, O:G.73, O:T.74, O:G.75, O:K.76, O:T.77, O:A.78, O:Y.366, B:R.353 Salt bridges: O:H.18, O:K.76, O:R.404, O:R.404 ADP.5: 17 residues within 4Å: Chain P: 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 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:A.24, P:V.47, P:G.80, P:T.81, P:G.82, P:K.83, P:T.84, P:A.85, P:N.329, P:Y.362, P:Y.362 Salt bridges: P:H.25, P:K.83, P:R.400, P:R.400 ADP.6: 20 residues within 4Å: Chain N: R.357 Chain Q: A.24, H.25, H.27, I.28, G.45, M.46, V.47, Q.78, P.79, G.80, G.82, K.83, T.84, A.85, Y.362, I.370, L.399, R.400, I.403 15 PLIP interactions: 14 interactions with chain Q, 1 interactions with chain N Hydrogen bonds: Q:A.24, Q:V.47, Q:G.80, Q:T.81, Q:G.82, Q:K.83, Q:T.84, Q:A.85, Q:Y.362, Q:Y.362, N:R.357 Salt bridges: Q:H.25, Q:K.83, Q:R.400, Q:R.400 ADP.7: 14 residues within 4Å: Chain R: Q.522, M.545, G.546, L.547, G.548, K.549, T.550, V.551, N.581, E.585, F.589, N.1184, R.1212, L.1213 15 PLIP interactions: 15 interactions with chain R Hydrogen bonds: R:Q.522, R:E.544, R:G.546, R:L.547, R:G.548, R:K.549, R:T.550, R:N.581, R:N.1184, R:N.1184, R:R.1212 Salt bridges: R:K.549, R:R.1212, R:R.1212 pi-Stacking: R:F.589

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

ATP.3: 20 residues within 4Å: Chain N: S.17, H.18, H.20, L.39, V.40, Q.42, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, D.302, E.303, Y.366, I.374, R.404 Chain P: R.353 22 PLIP interactions: 20 interactions with chain N, 2 interactions with chain P Hydrogen bonds: N:V.40, N:V.40, N:P.71, N:G.73, N:T.74, N:G.75, N:K.76, N:T.77, N:T.77, N:A.78, N:E.303, N:E.303, N:Y.366, N:R.404 Salt bridges: N:H.18, N:K.76, N:K.76, N:K.76, N:R.404, N:R.404, P:R.353, P:R.353

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-6. To Be Published

Release Date

2025-08-20

Peptides

RuvB-like 1: ANO
RuvB-like 2: BPQ
INO80 complex subunit C: C
Histone H3.1: FJ
Histone H4: GK
Histone H2A type 1-B/E: HL
Histone H2B type 2-E: IM
Chromatin-remodeling ATPase INO80: R
INO80 complex subunit B: S
Actin-related protein 5: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

N
A

O
B

B
E

P
D

Q
F

C
I

F
M

J
Q

G
N

K
R

H
O

L
S

I
P

M
T

R
G

S
H

T
J

RuvB-like 1

RuvB-like 2

INO80 complex subunit C

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 2-E

Chromatin-remodeling ATPase INO80

INO80 complex subunit B

Actin-related protein 5

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