› 4xmp

X-ray diffraction
1.78Å resolution

Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120

Released:
DOI: 10.2210/pdb4xmp/pdb
PDB entry 4xmp coloured by chain, front view.
PDB entry 4xmp coloured by chain, side view.
PDB entry 4xmp coloured by chain, top view.
Source organisms:
Primary publication:
Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.
Wu X, Zhang Z, Schramm CA, Joyce MG, Kwon YD, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L
Cell 161 470-485 (2015)
PMID: 25865483

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-134618 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 354 amino acids
Theoretical weight: 39.67 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8JDI3 (Residues: 43-122, 195-297, 319-481; Coverage: 41%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Immunoglobulin heavy constant gamma 1 Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 25.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01857 (Residues: 1-103; Coverage: 26%)
Gene name: IGHG1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Immunoglobulin kappa constant Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 23.01 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01834 (Residues: 1-107; Coverage: 100%)
Gene name: IGKC
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand NAG 11 x NAG
Ligand BU3 2 x BU3
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 69.713Å b: 82.496Å c: 163.066Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.201
Expression system: Homo sapiens

Quick links

Citations

34 review citations

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

6 mentions without citation

A matrix of structure-based designs yields improved VRC01-class antibodies for HIV-1 therapy and prevention.
Kwon et al. (2021)
5 more