› 4i3s

X-ray diffraction
2.85Å resolution

Crystal structure of the outer domain of HIV-1 gp120 in complex with VRC-PG04 space group P21

Released:
DOI: 10.2210/pdb4i3s/pdb
PDB entry 4i3s coloured by chain, front view.
PDB entry 4i3s coloured by chain, side view.
PDB entry 4i3s coloured by chain, top view.
Source organisms:
Primary publication:
Outer domain of HIV-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody VRC-PG04.
Joyce MG, Kanekiyo M, Xu L, Biertümpfel C, Boyington JC, Moquin S, Shi W, Wu X, Yang Y, Yang ZY, Zhang B, Zheng A, Zhou T, Zhu J, Mascola JR, Kwong PD, Nabel GJ
J Virol 87 2294-306 (2013)
PMID: 23236069

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212260 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 190 amino acids
Theoretical weight: 20.77 KDa
Source organism: Human immunodeficiency virus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3ZLH8 (Residues: 248-475; Coverage: 22%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Heavy chain of VRC-PG04 Fab Chain: H
Molecule details ›
Chain: H
Length: 228 amino acids
Theoretical weight: 24.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Light chain of VRC-PG04 Fab Chain: L
Molecule details ›
Chain: L
Length: 208 amino acids
Theoretical weight: 23.07 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 47.647Å b: 73.471Å c: 109.292Å
α: 90° β: 100.94° γ: 90°
R-values:
R R work R free
0.253 0.248 0.32
Expression system: Homo sapiens

Quick links

Citations

9 review citations

HIV-1 neutralizing antibodies: understanding nature's pathways.
Mascola et al. (2013)
8 more

4 mentions without citation

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.
Jardine et al. (2016)
3 more