› 1rzk

X-ray diffraction
2.9Å resolution

HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

Released:
DOI: 10.2210/pdb1rzk/pdb
PDB entry 1rzk coloured by chain, front view.
PDB entry 1rzk coloured by chain, side view.
PDB entry 1rzk coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120.
Huang CC, Venturi M, Majeed S, Moore MJ, Phogat S, Zhang MY, Dimitrov DS, Hendrickson WA, Robinson J, Sodroski J, Wyatt R, Choe H, Farzan M, Kwong PD
Proc Natl Acad Sci U S A 101 2706-11 (2004)
PMID: 14981267

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-208495 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Surface protein gp120 Chain: G
Molecule details ›
Chain: G
Length: 313 amino acids
Theoretical weight: 34.84 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P35961 (Residues: 81-479; Coverage: 38%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
T-cell surface glycoprotein CD4 Chain: C
Molecule details ›
Chain: C
Length: 185 amino acids
Theoretical weight: 20.5 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P01730 (Residues: 26-210; Coverage: 43%)
Gene name: CD4
Sequence domains:
Structure domains: Immunoglobulins
ANTIBODY 17B, LIGHT CHAIN Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.4 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
Structure domains: Immunoglobulins
ANTIBODY 17B, HEAVY CHAIN Chain: H
Molecule details ›
Chain: H
Length: 229 amino acids
Theoretical weight: 24.46 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 14 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: C2
Unit cell:
a: 174.98Å b: 81.71Å c: 74.48Å
α: 90° β: 90.37° γ: 90°
R-values:
R R work R free
0.205 0.205 0.297
Expression systems:
  • Drosophila melanogaster
  • Cricetulus griseus
  • Human gammaherpesvirus 4

Quick links

Citations

36 review citations

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

37 mentions without citation

On the irrationality of rational design of an HIV vaccine in light of protein intrinsic disorder.
Uversky VN. (2021)
36 more