› 4h0y

X-ray diffraction
1.94Å resolution

Crystal structure of NAD+-Ia(E380S)-actin complex

Released:
DOI: 10.2210/pdb4h0y/pdb
PDB entry 4h0y coloured by chain, front view.
PDB entry 4h0y coloured by chain, side view.
PDB entry 4h0y coloured by chain, top view.
Source organisms:
Primary publication:
Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex.
Tsurumura T, Tsumori Y, Qiu H, Oda M, Sakurai J, Nagahama M, Tsuge H
Proc Natl Acad Sci U S A 110 4267-72 (2013)
PMID: 23382240

Function and Biology Details

Reaction catalysed: 
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159305 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
ADP ribosyltransferase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 418 amino acids
Theoretical weight: 48.18 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46220 (Residues: 42-454; Coverage: 91%)
Sequence domains: ADP-ribosyltransferase exoenzyme
Structure domains: Toxin ADP-ribosyltransferase; Chain A, domain 1
Actin, alpha skeletal muscle Chain: B
Molecule details ›
Chain: B
Length: 375 amino acids
Theoretical weight: 41.86 KDa
Source organism: Oryctolagus cuniculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P68135 (Residues: 3-377; Coverage: 100%)
Gene names: ACTA, ACTA1
Sequence domains: Actin
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 1 x NAD
5 bound ligands:
Ligand PO4 1 x PO4
Ligand EDO 52 x EDO
Ligand CA 1 x CA
Ligand ATP 1 x ATP
Ligand LAR 1 x LAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 53.869Å b: 134.936Å c: 154.336Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.233
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Insights into the biogenesis, function, and regulation of ADP-ribosylation.
Cohen et al. (2018)
10 more

2 mentions without citation

Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination.
Kalayil et al. (2018)
1 more