› 5vgj

X-ray diffraction
3.46Å resolution

Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90, bound to a scaffolded WITO V1V2 domain

Released:
DOI: 10.2210/pdb5vgj/pdb
PDB entry 5vgj coloured by chain, front view.
PDB entry 5vgj coloured by chain, side view.
PDB entry 5vgj coloured by chain, top view.
Source organisms:
Primary publication:
Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.
Cale EM, Gorman J, Radakovich NA, Crooks ET, Osawa K, Tong T, Li J, Nagarajan R, Ozorowski G, Ambrozak DR, Asokan M, Bailer RT, Bennici AK, Chen X, Doria-Rose NA, Druz A, Feng Y, Joyce MG, Louder MK, O'Dell S, Oliver C, Pancera M, Connors M, Hope TJ, Kepler TB, Wyatt RT, Ward AB, Georgiev IS, Kwong PD, Mascola JR, Binley JM
Immunity 46 777-791.e10 (2017)
PMID: 28514685

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-231384 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 134 amino acids
Theoretical weight: 14.76 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q5G5U5 (Residues: 125-162, 163-221; Coverage: 11%)
Gene name: env
VRC38.01 Fab Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 236 amino acids
Theoretical weight: 25.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
VRC38.01 Fab Light Chain Chain: L
Molecule details ›
Chain: L
Length: 220 amino acids
Theoretical weight: 24.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 106.572Å b: 106.572Å c: 129.857Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.214 0.273
Expression system: Homo sapiens

Quick links

Citations

12 review citations

Recent progress in broadly neutralizing antibodies to HIV.
Sok et al. (2018)
11 more

4 mentions without citation

A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target.
Parker Miller et al. (2021)
3 more