6rny

Electron Microscopy
3.9Å resolution

PFV intasome - nucleosome strand transfer complex

Released:

Function and Biology Details

Reactions catalysed:
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-120559 (preferred)
Entry contents:
5 distinct polypeptide molecules
5 distinct DNA molecules
Macromolecules (10 distinct):
Histone H3.3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84243 (Residues: 1-136; Coverage: 100%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C0S8 (Residues: 1-130; Coverage: 100%)
Gene names: H2AC11, H2AC13, H2AC15, H2AC16, H2AC17, H2AFC, H2AFD, H2AFI, H2AFN, H2AFP, HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62807 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Sequence domains: Core histone H2A/H2B/H3/H4
Integrase Chains: K, L, O, P
Molecule details ›
Chains: K, L, O, P
Length: 395 amino acids
Theoretical weight: 44.46 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 754-1143; Coverage: 34%)
Gene name: pol
Sequence domains:
DNA (128-MER) Chain: I
Molecule details ›
Chain: I
Length: 128 nucleotides
Theoretical weight: 39.19 KDa
DNA (108-MER) Chain: U
Molecule details ›
Chain: U
Length: 108 nucleotides
Theoretical weight: 33.58 KDa
DNA (33-MER) Chain: T
Molecule details ›
Chain: T
Length: 33 nucleotides
Theoretical weight: 10.11 KDa
DNA (53-MER) Chain: J
Molecule details ›
Chain: J
Length: 53 nucleotides
Theoretical weight: 16.4 KDa
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3') Chains: M, Q
Molecule details ›
Chains: M, Q
Length: 19 nucleotides
Theoretical weight: 5.83 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-4960
Expression system: Escherichia coli