› 3tgq

X-ray diffraction
3.4Å resolution

Crystal structure of unliganded HIV-1 clade B strain YU2 gp120 core

Released:
DOI: 10.2210/pdb3tgq/pdb
PDB entry 3tgq coloured by chain, front view.
PDB entry 3tgq coloured by chain, side view.
PDB entry 3tgq coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.
Kwon YD, Finzi A, Wu X, Dogo-Isonagie C, Lee LK, Moore LR, Schmidt SD, Stuckey J, Yang Y, Zhou T, Zhu J, Vicic DA, Debnath AK, Shapiro L, Bewley CA, Mascola JR, Sodroski JG, Kwong PD
Proc Natl Acad Sci U S A 109 5663-8 (2012)
PMID: 22451932

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-153062 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Surface protein gp120 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 352 amino acids
Theoretical weight: 39.22 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P35961 (Residues: 43-479; Coverage: 43%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Ligands and Environments

1 bound ligand:
Ligand NAG 25 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P65
Unit cell:
a: 222.97Å b: 222.97Å c: 86.48Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.28 0.28 0.313
Expression system: Homo sapiens

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Citations

25 review citations

Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses.
Burton et al. (2012)
24 more

9 mentions without citation

HIV-1 envelope glycoprotein structure.
Merk et al. (2013)
8 more