› 5nbn

X-ray diffraction
4Å resolution

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

Released:
DOI: 10.2210/pdb5nbn/pdb
PDB entry 5nbn coloured by chain, front view.
PDB entry 5nbn coloured by chain, side view.
PDB entry 5nbn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP
Nat Struct Mol Biol 25 823-832 (2018)
PMID: 30177756

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-547065 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Actin-related protein 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 489 amino acids
Theoretical weight: 54.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P80428 (Residues: 1-489; Coverage: 100%)
Gene names: ACT3, ARP4, J1012, YJL081C
Sequence domains: Actin
Structure domains:
Actin Chains: C, D
Molecule details ›
Chains: C, D
Length: 375 amino acids
Theoretical weight: 41.75 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P60010 (Residues: 1-375; Coverage: 100%)
Gene names: ABY1, ACT1, END7, YFL039C
Sequence domains: Actin
Structure domains:
Actin-like protein ARP8 Chains: E, F
Molecule details ›
Chains: E, F
Length: 628 amino acids
Theoretical weight: 71.99 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12386 (Residues: 255-881; Coverage: 71%)
Gene names: ARP8, YOR141C, YOR3348C
Sequence domains: Actin
Structure domains:
Chromatin-remodeling ATPase INO80 Chains: G, H
Molecule details ›
Chains: G, H
Length: 147 amino acids
Theoretical weight: 18.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P53115 (Residues: 462-598; Coverage: 9%)
Gene names: G1880, INO80, YGL150C
Sequence domains: DNA-binding domain

Ligands and Environments

3 bound ligands:
Ligand CA 4 x CA
Ligand ATP 4 x ATP
Ligand LAR 2 x LAR
1 modified residue:
Ligand HIC 2 x HIC

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 172.294Å b: 263.909Å c: 241.402Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.193 0.242
Expression system: Trichoplusia ni

Quick links

Citations

12 review citations

Structure and Function of Chromatin Remodelers.
Reyes et al. (2021)
11 more

3 mentions without citation

INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling.
Willhoft et al. (2020)
2 more