› 2qad

X-ray diffraction
3.3Å resolution

Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4

Released:
DOI: 10.2210/pdb2qad/pdb
PDB entry 2qad coloured by chain, front view.
PDB entry 2qad coloured by chain, side view.
PDB entry 2qad coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4.
Huang CC, Lam SN, Acharya P, Tang M, Xiang SH, Hussan SS, Stanfield RL, Robinson J, Sodroski J, Wilson IA, Wyatt R, Bewley CA, Kwong PD
Science 317 1930-4 (2007)
PMID: 17901336

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero octamer
PDBe Complex ID:
PDB-CPX-207583 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Surface protein gp120 Chains: A, E
Molecule details ›
Chains: A, E
Length: 322 amino acids
Theoretical weight: 36.06 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P35961 (Residues: 88-479; Coverage: 40%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
T-cell surface glycoprotein CD4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 181 amino acids
Theoretical weight: 20.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01730 (Residues: 26-206; Coverage: 42%)
Gene name: CD4
Sequence domains:
Structure domains: Immunoglobulins
anti-HIV-1 antibody 412d light chain Chains: C, G
Molecule details ›
Chains: C, G
Length: 214 amino acids
Theoretical weight: 23.48 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chains: D, H
Molecule details ›
Chains: D, H
Length: 231 amino acids
Theoretical weight: 24.84 KDa
Source organism: Homo sapiens
Expression system: Human gammaherpesvirus 4
UniProt:
  • Canonical: A4F255 (Residues: 1-96, 97-114, 115-228; Coverage: 95%)
Gene name: VHCH1
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NAG 31 x NAG
Ligand MLA 4 x MLA
Ligand EDO 7 x EDO
1 modified residue:
Ligand TYS 4 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 109.6Å b: 53.021Å c: 225.326Å
α: 90° β: 104.64° γ: 90°
R-values:
R R work R free
0.202 0.202 0.269
Expression systems:
  • Homo sapiens
  • Escherichia coli
  • Human gammaherpesvirus 4

Quick links

Citations

38 review citations

Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme.
White et al. (2008)
37 more

63 mentions without citation

Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies.
Kufareva et al. (2015)
62 more