› 6b72

X-ray diffraction
3.2Å resolution

A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule

Released:
DOI: 10.2210/pdb6b72/pdb
PDB entry 6b72 coloured by chain, front view.
PDB entry 6b72 coloured by chain, side view.
PDB entry 6b72 coloured by chain, top view.
Source organism: HIV-1 M:B_ARV2/SF2
Primary publication:
A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding.
Wu M, Alvarado JJ, Augelli-Szafran CE, Ptak RG, Smithgall TE
PLoS One 13 e0192512 (2018)
PMID: 29415006

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136962 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C-terminal core protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 151 amino acids
Theoretical weight: 17.76 KDa
Source organism: HIV-1 M:B_ARV2/SF2
Expression system: Escherichia coli
UniProt:
  • Canonical: P03407 (Residues: 57-207; Coverage: 72%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef

Ligands and Environments

1 bound ligand:
Ligand BOG 3 x BOG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 109.577Å b: 109.577Å c: 247.04Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.234 0.233 0.251
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

HIV-1 Nef dimers short-circuit immune receptor signaling by activating Tec-family kinases at the host cell membrane.
Li et al. (2020)
2 more

2 mentions without citation

How HIV Nef Proteins Hijack Membrane Traffic To Promote Infection.
Buffalo et al. (2019)
1 more