› 4jpk

X-ray diffraction
2.4Å resolution

Crystal structure of the germline-targeting HIV-1 gp120 engineered outer domain eOD-GT6 in complex with a putative VRC01 germline precursor Fab

Released:
DOI: 10.2210/pdb4jpk/pdb
PDB entry 4jpk coloured by chain, front view.
PDB entry 4jpk coloured by chain, side view.
PDB entry 4jpk coloured by chain, top view.
Source organisms:
Primary publication:
Rational HIV immunogen design to target specific germline B cell receptors.
Jardine J, Julien JP, Menis S, Ota T, Kalyuzhniy O, McGuire A, Sok D, Huang PS, MacPherson S, Jones M, Nieusma T, Mathison J, Baker D, Ward AB, Burton DR, Stamatatos L, Nemazee D, Wilson IA, Schief WR
Science 340 711-6 (2013)
PMID: 23539181

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-209056 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Putative VRC01 germline precursor Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 248 amino acids
Theoretical weight: 26.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Putative VRC01 germline precursor Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 210 amino acids
Theoretical weight: 23.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Surface protein gp120 Chain: A
Molecule details ›
Chain: A
Length: 172 amino acids
Theoretical weight: 18.58 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P04578 (Residues: 254-399; Coverage: 14%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 179.26Å b: 63.3Å c: 61.3Å
α: 90° β: 90.43° γ: 90°
R-values:
R R work R free
0.203 0.2 0.263
Expression systems:
  • Escherichia coli
  • Homo sapiens

Quick links

Citations

162 review citations

HIV infection: epidemiology, pathogenesis, treatment, and prevention.
Maartens et al. (2014)
161 more

21 mentions without citation

Advances in structure-based vaccine design.
Kulp et al. (2013)
20 more