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Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA

Electron Microscopy
3.57Å resolution
PDB entry 8e40 coloured by chain, front view.
PDB entry 8e40 coloured by chain, side view.
PDB entry 8e40 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 3 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 37403.37 Å2
Buried surface area: 10319.59 Å2
Dissociation area: 2,133.4 Å2
Dissociation energy (ΔGdiss): -4.74 kcal/mol
Dissociation entropy (TΔSdiss): 26.32 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-223602

Macromolecules

DNA dC->dU-editing enzyme APOBEC-3G
Chain: A
Length: 386 amino acids
Theoretical weight: 45.19 KDa
Source organism: Macaca mulatta
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7YR23 (Residues: 9-377; Coverage: 95%)
Gene name: APOBEC3G
Pfam:
InterPro:
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8e40, assembly 1, front view.
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8e40, assembly 1, side view.
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8e40, assembly 1, top view.
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Virion infectivity factor
Chain: B
Length: 178 amino acids
Theoretical weight: 21.14 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P12504 (Residues: 1-176; Coverage: 92%)
Gene name: vif
Pfam: Retroviral Vif (Viral infectivity) protein
InterPro: Retroviral Vif (Viral infectivity) protein
Virion infectivity factor in PDB entry 8e40, assembly 1, front view.
Virion infectivity factor in PDB entry 8e40, assembly 1, side view.
Virion infectivity factor in PDB entry 8e40, assembly 1, top view.
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Core-binding factor subunit beta
Chain: C
Length: 157 amino acids
Theoretical weight: 18.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13951 (Residues: 1-157; Coverage: 86%)
Gene name: CBFB
Pfam: Core binding factor beta subunit
InterPro:
Core-binding factor subunit beta in PDB entry 8e40, assembly 1, front view.
Core-binding factor subunit beta in PDB entry 8e40, assembly 1, side view.
Core-binding factor subunit beta in PDB entry 8e40, assembly 1, top view.
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RNA chain R
Name: RNA
Representative chains: R
Length: 22 nucleotides
Theoretical weight: 6.88 KDa
RNA in PDB entry 8e40, assembly 1, front view.
RNA in PDB entry 8e40, assembly 1, side view.
RNA in PDB entry 8e40, assembly 1, top view.
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RNA chain r
Name: RNA
Representative chains: r
Length: 25 nucleotides
Theoretical weight: 8 KDa
RNA in PDB entry 8e40, assembly 1, front view.
RNA in PDB entry 8e40, assembly 1, side view.
RNA in PDB entry 8e40, assembly 1, top view.
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