SMTL ID : 8a5o.1

Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 17 residues within 4Å: Chain B: G.274, S.275, N.276, S.277, K.279, G.405, G.504, A.505, A.506, E.507, D.531, E.563, K.566, G.735, S.736, K.738 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.275, B:N.276, B:N.276, B:G.405, B:A.505, B:E.563, B:K.566, B:G.735, B:K.738 Salt bridges: B:K.279, B:K.279 pi-Cation interactions: B:K.567 AGS.3: 21 residues within 4Å: Chain C: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, F.306, K.336 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.15, C:M.16, C:D.157, C:D.157, C:K.213, C:E.214, C:E.214, C:G.302, C:T.303 Salt bridges: C:K.18, C:K.18 pi-Stacking: C:F.306 AGS.5: 18 residues within 4Å: Chain D: G.22, S.23, Y.24, T.25, G.78, G.161, H.162, D.163, T.164, Q.240, K.243, E.244, G.412, G.413, T.414, S.416, Q.449 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:S.23, D:Y.24, D:T.25, D:H.162, D:D.163, D:T.164, D:Q.240, D:K.243, D:G.413, D:T.414, D:S.416, D:Q.449

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain B: E.484, N.502 Ligands: AGS.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: Q.137 Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: AGS.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunert, F. et al., Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Sci Adv (2022)

Release Date

2022-12-14

Peptides

Chromatin-remodeling ATPase INO80: A
Actin-like protein ARP8: B
Actin: C
Actin-related protein 4: D
Ino eighty subunit 4: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
U

C
V

D
W

E
X

Chromatin-remodeling ATPase INO80

Actin-like protein ARP8

Actin

Actin-related protein 4

Ino eighty subunit 4

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