› 6rwl

Electron Microscopy
3.36Å resolution

SIVrcm intasome

Released:
DOI: 10.2210/pdb6rwl/pdb
PDB entry 6rwl coloured by chain, front view.
PDB entry 6rwl coloured by chain, side view.
PDB entry 6rwl coloured by chain, top view.
Source organism: Simian immunodeficiency virus
Primary publication:
Structural basis of second-generation HIV integrase inhibitor action and viral resistance.
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P
Science 367 806-810 (2020)
PMID: 32001525
Related structures: EMD-10041

Function and Biology Details

Reactions catalysed: 
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120579 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Pol protein Chains: A, B, C, E, I, J, K, M
Molecule details ›
Chains: A, B, C, E, I, J, K, M
Length: 290 amino acids
Theoretical weight: 32.73 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1ANT8 (Residues: 735-1023; Coverage: 28%)
Gene name: pol
Sequence domains:
Pol protein Chains: D, L
Molecule details ›
Chains: D, L
Length: 289 amino acids
Theoretical weight: 32.68 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1ANT8 (Residues: 735-1023; Coverage: 28%)
Gene name: pol
Sequence domains:
Pol protein Chains: F, N
Molecule details ›
Chains: F, N
Length: 290 amino acids
Theoretical weight: 32.69 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1ANT8 (Residues: 735-1023; Coverage: 28%)
Gene name: pol
Sequence domains:
DNA (5'-D(P*GP*CP*TP*AP*AP*GP*AP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*CP*CP*A)-3') Chains: T, W
Molecule details ›
Chains: T, W
Length: 30 nucleotides
Theoretical weight: 9.22 KDa
DNA (5'-D(*AP*AP*CP*TP*GP*GP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*TP*CP*TP*TP*AP*GP*C)-3') Chains: Q, S
Molecule details ›
Chains: Q, S
Length: 33 nucleotides
Theoretical weight: 10.13 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.36Å
Relevant EMDB volumes: EMD-10041
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Cryo-EM as a powerful tool for drug discovery.
Van Drie et al. (2020)
11 more

3 mentions without citation

Close-up: HIV/SIV intasome structures shed new light on integrase inhibitor binding and viral escape mechanisms.
Engelman et al. (2021)
2 more