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Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5

Electron Microscopy
3.24Å resolution
PDB entry 8fvi coloured by chain, front view.
PDB entry 8fvi coloured by chain, side view.
PDB entry 8fvi coloured by chain, top view.
Source organisms:
Assembly composition:
hetero octamer (preferred)
Entry contents: 6 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero octamer
Accessible surface area: 38872.36 Å2
Buried surface area: 14288.57 Å2
Dissociation area: 715.43 Å2
Dissociation energy (ΔGdiss): -11.14 kcal/mol
Dissociation entropy (TΔSdiss): 13.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-240493

Macromolecules

Core-binding factor subunit beta
Chain: 0
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
Core-binding factor subunit beta in PDB entry 8fvi, assembly 1, front view.
Core-binding factor subunit beta in PDB entry 8fvi, assembly 1, side view.
Core-binding factor subunit beta in PDB entry 8fvi, assembly 1, top view.
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Virion infectivity factor
Chain: 1
Length: 178 amino acids
Theoretical weight: 21.16 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
Virion infectivity factor in PDB entry 8fvi, assembly 1, front view.
Virion infectivity factor in PDB entry 8fvi, assembly 1, side view.
Virion infectivity factor in PDB entry 8fvi, assembly 1, top view.
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DNA dC->dU-editing enzyme APOBEC-3H
Chain: A
Length: 189 amino acids
Theoretical weight: 22.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6NTF7 (Residues: 1-181; Coverage: 91%)
  • Best match: Q6NTF7-2 (Residues: 1-181)
Gene name: APOBEC3H
Pfam: APOBEC3
DNA dC->dU-editing enzyme APOBEC-3H in PDB entry 8fvi, assembly 1, front view.
DNA dC->dU-editing enzyme APOBEC-3H in PDB entry 8fvi, assembly 1, side view.
DNA dC->dU-editing enzyme APOBEC-3H in PDB entry 8fvi, assembly 1, top view.
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Cullin-5
Chain: x
Length: 314 amino acids
Theoretical weight: 36.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93034 (Residues: 11-320; Coverage: 40%)
Gene names: CUL5, VACM1
Pfam: Cullin family
Cullin-5 in PDB entry 8fvi, assembly 1, front view.
Cullin-5 in PDB entry 8fvi, assembly 1, side view.
Cullin-5 in PDB entry 8fvi, assembly 1, top view.
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Elongin-B
Chain: y
Length: 102 amino acids
Theoretical weight: 11.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-102; Coverage: 86%)
Gene names: ELOB, TCEB2
Pfam: Ubiquitin family
Elongin-B in PDB entry 8fvi, assembly 1, front view.
Elongin-B in PDB entry 8fvi, assembly 1, side view.
Elongin-B in PDB entry 8fvi, assembly 1, top view.
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Elongin-C
Chain: z
Length: 96 amino acids
Theoretical weight: 10.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Pfam: Skp1 family, tetramerisation domain
Elongin-C in PDB entry 8fvi, assembly 1, front view.
Elongin-C in PDB entry 8fvi, assembly 1, side view.
Elongin-C in PDB entry 8fvi, assembly 1, top view.
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RNA chain B
Name: RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Representative chains: B
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') in PDB entry 8fvi, assembly 1, front view.
RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') in PDB entry 8fvi, assembly 1, side view.
RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') in PDB entry 8fvi, assembly 1, top view.
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RNA chain C
Name: RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Representative chains: C
Length: 9 nucleotides
Theoretical weight: 2.92 KDa
RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') in PDB entry 8fvi, assembly 1, front view.
RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') in PDB entry 8fvi, assembly 1, side view.
RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') in PDB entry 8fvi, assembly 1, top view.
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