SMTL ID : 9ge5.1

CryoEM structure of the human INO80-Hexasome complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.35 Å

Oligo State

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

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: S.16, H.17, H.19, G.37, L.38, V.39, P.71, G.72, T.73, G.74, K.75, T.76, A.77, E.302, N.331, Y.365, I.373, L.402, R.403 Chain D: R.339 22 PLIP interactions: 2 interactions with chain D, 20 interactions with chain A Salt bridges: D:R.339, D:R.339, A:H.17, A:K.75, A:K.75, A:R.403, A:R.403 Hydrogen bonds: A:S.16, A:S.16, A:V.39, A:V.39, A:G.72, A:T.73, A:T.73, A:G.74, A:K.75, A:T.76, A:T.76, A:A.77, A:E.302, A:N.331, A:Y.365

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

ADP.2: 19 residues within 4Å: Chain B: S.16, H.17, H.19, G.37, L.38, V.39, Q.41, P.70, P.71, G.72, T.73, G.74, K.75, T.76, A.77, Y.365, I.373, L.402, R.403 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.16, B:H.17, B:V.39, B:G.72, B:T.73, B:G.74, B:K.75, B:T.76, B:T.76, B:A.77, B:Y.365, B:Y.365 Salt bridges: B:H.17, B:K.75, B:R.403, B:R.403 ADP.3: 17 residues within 4Å: Chain C: S.16, H.17, H.19, G.37, L.38, V.39, P.71, G.72, T.73, G.74, K.75, T.76, A.77, Y.365, I.373, L.402, R.403 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.16, C:H.17, C:V.39, C:V.39, C:G.72, C:T.73, C:G.74, C:K.75, C:T.76, C:T.76, C:T.76, C:A.77, C:Y.365 Salt bridges: C:H.17, C:K.75, C:R.403, C:R.403 ADP.4: 18 residues within 4Å: Chain B: R.356 Chain D: A.10, H.11, H.13, M.32, V.33, P.65, G.66, T.67, G.68, K.69, T.70, A.71, Y.348, I.356, L.385, R.386, I.389 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:A.10, D:V.33, D:V.33, D:G.66, D:G.68, D:T.70, D:T.70, D:A.71, D:Y.348 Salt bridges: D:K.69, D:R.386, D:R.386, B:R.356 ADP.5: 17 residues within 4Å: Chain E: A.10, H.11, H.13, G.31, M.32, V.33, P.65, G.66, T.67, G.68, K.69, T.70, A.71, Y.348, I.356, L.385, R.386 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:H.11, E:V.33, E:G.66, E:T.67, E:G.68, E:K.69, E:T.70, E:T.70, E:A.71, E:Y.348, E:Y.348, C:E.319 Salt bridges: E:H.11, E:K.69, E:R.386, E:R.386 ADP.6: 19 residues within 4Å: Chain A: R.356 Chain F: A.10, H.11, H.13, G.31, M.32, V.33, P.65, G.66, T.67, G.68, K.69, T.70, A.71, Y.348, I.356, L.385, R.386, I.389 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:H.11, F:V.33, F:V.33, F:G.66, F:T.67, F:G.68, F:K.69, F:T.70, F:T.70, F:A.71, F:Y.348, A:R.356 Salt bridges: F:H.11, F:K.69, F:R.386, F:R.386 ADP.7: 10 residues within 4Å: Chain G: G.29, L.30, G.31, K.32, R.71, F.72, N.667, R.695, L.696, G.697 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.29, G:L.30, G:G.31, G:K.32, G:R.71, G:R.71, G:N.667 Salt bridges: G:R.695 ADP.9: 12 residues within 4Å: Chain J: N.31, G.32, F.34, R.37, T.129, D.160, S.182, G.183, Y.184, H.241, G.490, V.524 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:N.31, J:N.31, J:F.34, J:T.129, J:Y.184, J:H.241, J:G.490 Salt bridges: J:R.37

1 x ZN: ZINC ION(Non-functional Binders)

ZN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aggarwal, P. et al., Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. 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: MO
Histone H4: NP
Histone H2A type 1-B/E: Q
Histone H2B type 1-B: R

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

O
Q

N
N

P
R

Q
S

R
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 1-B

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