› 5cd5

X-ray diffraction
3.4Å resolution

Crystal structure of an immature VRC01-class antibody DRVIA7 from a Chinese donor bound to clade A/E HIV-1 gp120 core

Released:
DOI: 10.2210/pdb5cd5/pdb
PDB entry 5cd5 coloured by chain, front view.
PDB entry 5cd5 coloured by chain, side view.
PDB entry 5cd5 coloured by chain, top view.
Source organisms:
Primary publication:
Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Kong L, Ju B, Chen Y, He L, Ren L, Liu J, Hong K, Su B, Wang Z, Ozorowski G, Ji X, Hua Y, Chen Y, Deller MC, Hao Y, Feng Y, Garces F, Wilson R, Dai K, O'Dell S, McKee K, Mascola JR, Ward AB, Wyatt RT, Li Y, Wilson IA, Zhu J, Shao Y
Immunity 44 939-50 (2016)
PMID: 27067056

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-207308 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 39.21 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0M3KKW9 (Residues: 1-353; Coverage: 100%)
Gene name: HIV-1 Env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
DRVIA7 Fab Heavy Chain Chain: C
Molecule details ›
Chain: C
Length: 220 amino acids
Theoretical weight: 24.05 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
DRVIA7 Fab Light Chain Chain: D
Molecule details ›
Chain: D
Length: 210 amino acids
Theoretical weight: 23.21 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 6 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P41212
Unit cell:
a: 72.325Å b: 72.325Å c: 338.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.269 0.253 0.306
Expression system: Homo sapiens

Quick links

Citations

11 review citations

Identification and specificity of broadly neutralizing antibodies against HIV.
McCoy et al. (2017)
10 more

2 mentions without citation

Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Kong et al. (2016)
1 more