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Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1

Electron Microscopy
3.3Å resolution
PDB entry 8cx1 coloured by chain, front view.
PDB entry 8cx1 coloured by chain, side view.
PDB entry 8cx1 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero dodecamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero dodecamer
Accessible surface area: 87443.8 Å2
Buried surface area: 29990.25 Å2
Dissociation area: 5,357.49 Å2
Dissociation energy (ΔGdiss): 5.36 kcal/mol
Dissociation entropy (TΔSdiss): 63.26 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-227154

Macromolecules

DNA dC->dU-editing enzyme APOBEC-3G
Chains: A, F
Length: 421 amino acids
Theoretical weight: 50.03 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9HC16 (Residues: 1-384; Coverage: 100%)
Gene names: APOBEC3G, MDS019
Pfam:
InterPro:
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8cx1, assembly 1, front view.
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8cx1, assembly 1, side view.
DNA dC->dU-editing enzyme APOBEC-3G in PDB entry 8cx1, assembly 1, top view.
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Virion infectivity factor
Chains: B, G
Length: 192 amino acids
Theoretical weight: 22.56 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P69723 (Residues: 1-192; Coverage: 100%)
Gene name: vif
Pfam: Retroviral Vif (Viral infectivity) protein
InterPro: Retroviral Vif (Viral infectivity) protein
Virion infectivity factor in PDB entry 8cx1, assembly 1, front view.
Virion infectivity factor in PDB entry 8cx1, assembly 1, side view.
Virion infectivity factor in PDB entry 8cx1, assembly 1, top view.
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Core-binding factor subunit beta
Chains: C, H
Length: 182 amino acids
Theoretical weight: 21.54 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13951 (Residues: 1-182; Coverage: 100%)
Gene name: CBFB
Pfam: Core binding factor beta subunit
InterPro:
Core-binding factor subunit beta in PDB entry 8cx1, assembly 1, front view.
Core-binding factor subunit beta in PDB entry 8cx1, assembly 1, side view.
Core-binding factor subunit beta in PDB entry 8cx1, assembly 1, top view.
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Elongin-B
Chains: D, I
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Pfam: Ubiquitin family
InterPro:
Elongin-B in PDB entry 8cx1, assembly 1, front view.
Elongin-B in PDB entry 8cx1, assembly 1, side view.
Elongin-B in PDB entry 8cx1, assembly 1, top view.
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Elongin-C
Chains: E, J
Length: 112 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q15369 (Residues: 1-112; Coverage: 100%)
Gene names: ELOC, TCEB1
Pfam: Skp1 family, tetramerisation domain
InterPro:
Elongin-C in PDB entry 8cx1, assembly 1, front view.
Elongin-C in PDB entry 8cx1, assembly 1, side view.
Elongin-C in PDB entry 8cx1, assembly 1, top view.
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RNA chain K
Name: RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3')
Representative chains: K
Length: 8 nucleotides
Theoretical weight: 2.5 KDa
RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, front view.
RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, side view.
RNA (5'-R(P*UP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, top view.
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RNA chain L
Name: RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3')
Representative chains: L
Length: 8 nucleotides
Theoretical weight: 2.52 KDa
RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, front view.
RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, side view.
RNA (5'-R(P*AP*AP*AP*AP*UP*AP*UP*U)-3') in PDB entry 8cx1, assembly 1, top view.
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