› 3jca

Electron Microscopy
4.8Å resolution

Core model of the Mouse Mammary Tumor Virus intasome

Released:
DOI: 10.2210/pdb3jca/pdb
PDB entry 3jca coloured by chain, front view.
PDB entry 3jca coloured by chain, side view.
PDB entry 3jca coloured by chain, top view.
Source organism: Mouse mammary tumor virus
Primary publication:
Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function.
Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN
Nature 530 358-61 (2016)
PMID: 26887496
Related structures: EMD-6441

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116429 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Integrase Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 265 amino acids
Theoretical weight: 30.03 KDa
Source organism: Mouse mammary tumor virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P03365 (Residues: 1437-1701; Coverage: 15%)
Gene name: gag-pro-pol
Sequence domains:
Integrase Chains: C, D, G, H
Molecule details ›
Chains: C, D, G, H
Length: 49 amino acids
Theoretical weight: 5.57 KDa
Source organism: Mouse mammary tumor virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P03365 (Residues: 1653-1701; Coverage: 3%)
Gene name: gag-pro-pol
Sequence domains: Integrase DNA binding domain
5'-D(*AP*AP*TP*GP*CP*CP*GP*CP*AP*GP*TP*CP*GP*GP*CP*CP*GP*AP*CP*CP*TP*G)-3' Chains: I, K
Molecule details ›
Chains: I, K
Length: 22 nucleotides
Theoretical weight: 6.74 KDa
5'-D(*CP*AP*GP*GP*TP*CP*GP*GP*CP*CP*GP*AP*CP*TP*GP*CP*GP*GP*CP*A)-3' Chains: J, L
Molecule details ›
Chains: J, L
Length: 20 nucleotides
Theoretical weight: 6.16 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.8Å
Relevant EMDB volumes: EMD-6441
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
15 more

12 mentions without citation

Practical lessons from protein structure prediction.
Ginalski et al. (2005)
11 more