› 4npy

X-ray diffraction
1.8Å resolution

Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive and potent HIV-1 neutralizing antibody

Released:
DOI: 10.2210/pdb4npy/pdb
Model geometry
Fit model/data
PDB entry 4npy coloured by chain, front view.
PDB entry 4npy coloured by chain, side view.
PDB entry 4npy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.
Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P
OpenAccess logo PLoS Pathog 9 e1003754 (2013)
PMID: 24278016

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179697 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ig-like domain-containing protein Chains: A, L
Molecule details ›
Chains: A, L
Length: 215 amino acids
Theoretical weight: 22.89 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6GMX6 (Residues: 31-81, 82-114, 115-176, 177-206, 207-238; Coverage: 44%)
Gene name: IGH@
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: B, H
Molecule details ›
Chains: B, H
Length: 235 amino acids
Theoretical weight: 25.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6GMX6 (Residues: 20-116, 117-118, 119-122, 123-238; Coverage: 49%)
Gene name: IGH@
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand GOL 3 x GOL
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 53.72Å b: 54.9Å c: 320.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.22
Expression system: Homo sapiens

Quick links

Citations

42 review citations

Broadly Neutralizing Antibodies to HIV and Their Role in Vaccine Design.
Burton et al. (2016)
41 more

5 mentions without citation

Genetic and structural analyses of affinity maturation in the humoral response to HIV-1.
Kepler et al. (2017)
4 more