› 4jdt

X-ray diffraction
3.26Å resolution

Crystal structure of chimeric germ-line precursor of NIH45-46 Fab in complex with gp120 of 93TH057 HIV-1

Released:
DOI: 10.2210/pdb4jdt/pdb
PDB entry 4jdt coloured by chain, front view.
PDB entry 4jdt coloured by chain, side view.
PDB entry 4jdt coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for HIV-1 gp120 recognition by a germ-line version of a broadly neutralizing antibody.
Scharf L, West AP, Gao H, Lee T, Scheid JF, Nussenzweig MC, Bjorkman PJ, Diskin R
Proc Natl Acad Sci U S A 110 6049-54 (2013)
PMID: 23524883

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-211969 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 361 amino acids
Theoretical weight: 40.2 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q0ED31 (Residues: 43-486; Coverage: 41%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 232 amino acids
Theoretical weight: 25.19 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 210 amino acids
Theoretical weight: 23 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 65.664Å b: 69.815Å c: 207.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.227 0.267
Expression systems:
  • Spodoptera frugiperda
  • Homo sapiens

Quick links

Citations

10 review citations

Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning.
Kwong et al. (2013)
9 more

6 mentions without citation

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