› 6o3j

X-ray diffraction
3.42Å resolution

Crystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1 in complex with its MPER peptide epitope (region 671-683 of HIV-1 gp41) and phosphatidic acid (06:0 PA)

Released:
DOI: 10.2210/pdb6o3j/pdb
PDB entry 6o3j coloured by chain, front view.
PDB entry 6o3j coloured by chain, side view.
PDB entry 6o3j coloured by chain, top view.
Source organisms:
Primary publication:
An MPER antibody neutralizes HIV-1 using germline features shared among donors.
Zhang L, Irimia A, He L, Landais E, Rantalainen K, Leaman DP, Vollbrecht T, Stano A, Sands DI, Kim AS, Poignard P, Burton DR, Murrell B, Ward AB, Zhu J, Wilson IA, Zwick MB
Nat Commun 10 5389 (2019)
PMID: 31772165

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231710 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
PGZL1 light chain Chains: B, L
Molecule details ›
Chains: B, L
Length: 215 amino acids
Theoretical weight: 23.3 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
PGZL1 heavy chain Chains: A, H
Molecule details ›
Chains: A, H
Length: 227 amino acids
Theoretical weight: 23.91 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Transmembrane protein gp41 Chains: G, I
Molecule details ›
Chains: G, I
Length: 16 amino acids
Theoretical weight: 2.19 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04578 (Residues: 671-683; Coverage: 2%)
Gene name: env

Ligands and Environments

2 bound ligands:
Ligand 44E 2 x 44E
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 181.859Å b: 43.931Å c: 154.526Å
α: 90° β: 92.49° γ: 90°
R-values:
R R work R free
0.217 0.214 0.264
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

9 review citations

Major Scientific Hurdles in HIV Vaccine Development: Historical Perspective and Future Directions.
Ng'uni et al. (2020)
8 more

1 mention without citation

Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack.
Yang et al. (2022)