› 7xn4

Electron Microscopy
3.35Å resolution

Cryo-EM structure of CopC-CaM-caspase-3 with NAD+

Released:
DOI: 10.2210/pdb7xn4/pdb
PDB entry 7xn4 coloured by chain, front view.
PDB entry 7xn4 coloured by chain, side view.
PDB entry 7xn4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin.
Zhang K, Peng T, Tao X, Tian M, Li Y, Wang Z, Ma S, Hu S, Pan X, Xue J, Luo J, Wu Q, Fu Y, Li S
Mol Cell (2022)
PMID: 36423631
Related structures: EMD-33310

Function and Biology Details

Reaction catalysed: 
Strict requirement for an Asp residue at positions P1 and P4. It has a preferred cleavage sequence of Asp-Xaa-Xaa-Asp-|- with a hydrophobic amino-acid residue at P2 and a hydrophilic amino-acid residue at P3, although Val or Ala are also accepted at this position
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-534417 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Caspase-3 Chains: A, C
Molecule details ›
Chains: A, C
Length: 277 amino acids
Theoretical weight: 31.65 KDa
Source organism: Homo sapiens
Expression system: Bacteria Latreille et al. 1825
UniProt:
  • Canonical: P42574 (Residues: 1-277; Coverage: 100%)
Gene names: CASP3, CPP32
Sequence domains: Caspase domain
Arginine ADP-riboxanase CopC Chain: B
Molecule details ›
Chain: B
Length: 487 amino acids
Theoretical weight: 52.99 KDa
Source organism: Chromobacterium violaceum
Expression system: Bacteria Latreille et al. 1825
UniProt:
  • Canonical: Q7NWF2 (Residues: 1-487; Coverage: 100%)
Gene names: CV_2038, copC
Sequence domains:
Calmodulin-1 Chain: D
Molecule details ›
Chain: D
Length: 149 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Bacteria Latreille et al. 1825
UniProt:
  • Canonical: P0DP23 (Residues: 1-149; Coverage: 100%)
Gene names: CALM, CALM1, CAM, CAM1
Sequence domains: EF-hand domain pair

Ligands and Environments

1 bound ligand:
Ligand NAD 1 x NAD
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.35Å
Relevant EMDB volumes: EMD-33310
Expression system: Bacteria Latreille et al. 1825

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