› 3ngb

X-ray diffraction
2.68Å resolution

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

Released:
DOI: 10.2210/pdb3ngb/pdb
PDB entry 3ngb coloured by chain, front view.
PDB entry 3ngb coloured by chain, side view.
PDB entry 3ngb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01.
Zhou T, Georgiev I, Wu X, Yang ZY, Dai K, Finzi A, Kwon YD, Scheid JF, Shi W, Xu L, Yang Y, Zhu J, Nussenzweig MC, Sodroski J, Shapiro L, Nabel GJ, Mascola JR, Kwong PD
Science 329 811-7 (2010)
PMID: 20616231

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-211965 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Envelope glycoprotein gp160 Chains: A, D, G, I
Molecule details ›
Chains: A, D, G, I
Length: 353 amino acids
Theoretical weight: 39.21 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q0ED31 (Residues: 43-122, 201-303, 325-486; Coverage: 40%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
Antigen binding fragment of heavy chain: Antibody VRC01 Chains: B, E, H, J
Molecule details ›
Chains: B, E, H, J
Length: 224 amino acids
Theoretical weight: 24.37 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Antigen binding fragment of light chain: Antibody VRC01 Chains: C, F, K, L
Molecule details ›
Chains: C, F, K, L
Length: 210 amino acids
Theoretical weight: 23.17 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
Carbohydrate polymer
3 bound ligands:
Ligand NAG 46 x NAG
Ligand BGC 13 x BGC
Ligand TRS 7 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 108.63Å b: 98.275Å c: 205.256Å
α: 90° β: 99.68° γ: 90°
R-values:
R R work R free
0.2 0.197 0.256
Expression system: Homo sapiens

Quick links

Citations

159 review citations

HIV-1 neutralizing antibodies: understanding nature's pathways.
Mascola et al. (2013)
158 more

87 mentions without citation

The structural biology of HIV-1: mechanistic and therapeutic insights.
Engelman et al. (2012)
86 more