› 8fvi

Electron Microscopy
3.24Å resolution

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

Released:
DOI: 10.2210/pdb8fvi/pdb
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:
Primary publication:
Structural basis of HIV-1 Vif-mediated E3 ligase targeting of host APOBEC3H.
Ito F, Alvarez-Cabrera AL, Kim K, Zhou ZH, Chen XS
OpenAccess logo Nat Commun 14 5241 (2023)
PMID: 37640699
Related structures: EMD-29488

Function and Biology Details

Reaction catalysed: 
Cytosine in single-stranded DNA + H(2)O = uracil in single-stranded DNA + NH(3)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-240493 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (8 distinct):
Core-binding factor subunit beta Chain: 0
Molecule details ›
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
Sequence domains: Core binding factor beta subunit
Virion infectivity factor Chain: 1
Molecule details ›
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
Sequence domains: Retroviral Vif (Viral infectivity) protein
DNA dC->dU-editing enzyme APOBEC-3H Chain: A
Molecule details ›
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
Sequence domains: APOBEC3
Cullin-5 Chain: x
Molecule details ›
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
Sequence domains: Cullin family
Elongin-B Chain: y
Molecule details ›
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
Sequence domains: Ubiquitin family
Elongin-C Chain: z
Molecule details ›
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
Sequence domains: Skp1 family, tetramerisation domain
RNA(5'-R(AP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
RNA(5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.92 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.24Å
Relevant EMDB volumes: EMD-29488
Expression system: Escherichia coli

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