› 6p59

X-ray diffraction
2.94Å resolution

Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex

Released:
DOI: 10.2210/pdb6p59/pdb
PDB entry 6p59 coloured by chain, front view.
PDB entry 6p59 coloured by chain, side view.
PDB entry 6p59 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for a Species-Specific Determinant of an SIV Vif Protein toward Hominid APOBEC3G Antagonism.
Binning JM, Chesarino NM, Emerman M, Gross JD
Cell Host Microbe 26 739-747.e4 (2019)
PMID: 31830442

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-122739 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Core-binding factor subunit beta Chains: A, C
Molecule details ›
Chains: A, C
Length: 165 amino acids
Theoretical weight: 19.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13951 (Residues: 1-165; Coverage: 91%)
Gene name: CBFB
Sequence domains: Core binding factor beta subunit
Elongin-B Chains: D, W
Molecule details ›
Chains: D, W
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chains: E, Z
Molecule details ›
Chains: E, Z
Length: 112 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 1-112; Coverage: 100%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
Virion infectivity factor Chains: B, F
Molecule details ›
Chains: B, F
Length: 220 amino acids
Theoretical weight: 25.62 KDa
Source organism: Simian immunodeficiency virus
Expression system: Escherichia coli
UniProt:
  • Canonical: E1ANT9 (Residues: 1-220; Coverage: 100%)
Gene name: vif
Sequence domains: Retroviral Vif (Viral infectivity) protein

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 2 x GOL
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 110.22Å b: 112.489Å c: 125.697Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.235 0.268
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structural Insights into APOBEC3-Mediated Lentiviral Restriction.
Delviks-Frankenberry et al. (2020)
6 other articles

4 mentions without citation

Examination of the APOBEC3 Barrier to Cross Species Transmission of Primate Lentiviruses.
Gaba et al. (2021)
3 more