› 7w4z

X-ray diffraction
1.15Å resolution

Crystal structure of fragmin domain-1 in complex with actin (AMPPNP-form)

Released:
DOI: 10.2210/pdb7w4z/pdb
PDB entry 7w4z coloured by chain, front view.
PDB entry 7w4z coloured by chain, side view.
PDB entry 7w4z coloured by chain, top view.
Source organisms:
Primary publication:
Structures and mechanisms of actin ATP hydrolysis.
Kanematsu Y, Narita A, Oda T, Koike R, Ota M, Takano Y, Moritsugu K, Fujiwara I, Tanaka K, Komatsu H, Nagae T, Watanabe N, Iwasa M, Maéda Y, Takeda S
OpenAccess logo Proc Natl Acad Sci U S A 119 e2122641119 (2022)
PMID: 36252034

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159344 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Actin, alpha skeletal muscle Chain: A
Molecule details ›
Chain: A
Length: 377 amino acids
Theoretical weight: 42.11 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P68139 (Residues: 1-377; Coverage: 100%)
Gene names: ACTA, ACTA1
Sequence domains: Actin
Gelsolin-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 162 amino acids
Theoretical weight: 18.25 KDa
Source organism: Physarum polycephalum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q94707 (Residues: 1-160; Coverage: 43%)
Sequence domains: Gelsolin repeat

Ligands and Environments

5 bound ligands:
Ligand ANP 1 x ANP
Ligand MG 1 x MG
Ligand PO4 2 x PO4
Ligand EDO 3 x EDO
Ligand CA 2 x CA
1 modified residue:
Ligand HIC 1 x HIC

Experiments and Validation Details

Entry percentile scores
X-ray source: AichiSR BEAMLINE BL2S1
Spacegroup: P212121
Unit cell:
a: 57.09Å b: 91.07Å c: 114.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.144 0.143 0.158
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Simulation toolkits at the molecular scale for trans-scale thermal signaling.
Kurisaki et al. (2023)
1 other article

1 mention without citation

Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis.
Iwasa et al. (2023)