SMTL ID : 6hts.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: S.17, H.18, H.20, G.38, L.39, V.40, G.41, P.71, P.72, G.73, T.74, G.75, K.76, T.77, A.78, Y.366, I.374, R.378, R.404 Chain B: E.317, R.353 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.17, A:H.20, A:V.40, A:G.73, A:T.74, A:G.75, A:K.76, A:T.77, A:T.77, A:A.78, A:Y.366, A:R.378 Salt bridges: A:H.18, A:K.76, A:R.404, A:R.404, B:R.353, B:R.353 ADP.2: 21 residues within 4Å: Chain B: A.24, H.27, G.45, M.46, V.47, Q.78, P.79, G.80, T.81, G.82, K.83, T.84, A.85, N.329, Y.362, I.370, R.374, R.400, I.403 Chain C: E.320, R.357 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.24, B:V.47, B:Q.78, B:G.80, B:T.81, B:G.82, B:K.83, B:T.84, B:A.85, B:N.329, B:Y.362, B:Y.362, B:R.374, B:R.400, C:E.320, C:R.357 Salt bridges: B:R.400 pi-Stacking: B:Y.362 ADP.3: 18 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, Y.366, I.374, R.404 Chain D: R.314, R.353 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.17, C:S.17, C:V.40, C:G.73, C:T.74, C:T.74, C:G.75, C:K.76, C:T.77, C:Y.366, C:Y.366, D:R.314 Salt bridges: C:K.76, C:R.404, D:R.314, D:R.353 ADP.4: 19 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, I.370, R.374, L.399, R.400, I.403 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:A.24, D:V.47, D:Q.78, D:G.80, D:T.81, D:T.81, D:G.82, D:K.83, D:T.84, D:Y.362, D:R.374 Salt bridges: D:H.25, D:K.83, 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, Y.366, I.374, R.378, R.404 Chain F: E.317, R.353 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.17, E:H.18, E:V.40, E:P.71, E:G.73, E:T.74, E:T.74, E:G.75, E:K.76, E:T.77, E:T.77, E:Y.366, E:Y.366, E:R.378 Salt bridges: E:H.18, E:K.76, E:R.404, F:R.353 ADP.6: 16 residues within 4Å: Chain A: E.320 Chain F: 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, R.400 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:A.24, F:H.25, F:V.47, F:G.80, F:T.81, F:T.81, F:G.82, F:K.83, F:T.84, F:Y.362, A:R.357 Salt bridges: F:H.25, F:R.400

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain Q: C.309, C.314, C.330, C.334 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.309, Q:C.314, Q:C.330, Q:C.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ayala, R. et al., Structure and regulation of the human INO80-nucleosome complex. Nature (2018)

Release Date

2018-11-07

Peptides

RuvB-like 1: ACE
RuvB-like 2: BDF
Chromatin-remodeling ATPase INO80: G
Actin-related protein 5: H
Histone H3.1: IM
Histone H4: JN
Histone H2A type 1-B/E: KO
Histone H2B type 1-J: LP
INO80 complex subunit B: Q

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

I
I

M
M

J
J

N
N

K
K

O
O

L
L

P
P

Q
R

RuvB-like 1

RuvB-like 2

Chromatin-remodeling ATPase INO80

Actin-related protein 5

Histone H3.1

Histone H4

Histone H2A type 1-B/E

Histone H2B type 1-J

INO80 complex subunit B

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