› 4rx4

X-ray diffraction
3.45Å resolution

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1 clade A Q842.d12 gp120

Released:
DOI: 10.2210/pdb4rx4/pdb
PDB entry 4rx4 coloured by chain, front view.4rx4 coloured by chain, front view. This structure contains:
  • 2 copies of Envelope glycoprotein gp160;
  • 2 copies of 8ANC134 Heavy chain;
  • 2 copies of 8ANC134 Light Chain;
  • 11 copies of 2-acetamido-2-deoxy-beta-D-glucopyranose;
  • 12 copies of SULFATE ION;
  • 5 copies of 1,2-ETHANEDIOL.
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PDB entry 4rx4 coloured by chain, side view.4rx4 coloured by chain, side view. This structure contains:
  • 2 copies of Envelope glycoprotein gp160;
  • 2 copies of 8ANC134 Heavy chain;
  • 2 copies of 8ANC134 Light Chain;
  • 11 copies of 2-acetamido-2-deoxy-beta-D-glucopyranose;
  • 12 copies of SULFATE ION;
  • 5 copies of 1,2-ETHANEDIOL.
">
PDB entry 4rx4 coloured by chain, top view.4rx4 coloured by chain, top view. This structure contains:
  • 2 copies of Envelope glycoprotein gp160;
  • 2 copies of 8ANC134 Heavy chain;
  • 2 copies of 8ANC134 Light Chain;
  • 11 copies of 2-acetamido-2-deoxy-beta-D-glucopyranose;
  • 12 copies of SULFATE ION;
  • 5 copies of 1,2-ETHANEDIOL.
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Source organisms:
Primary publication:
Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.
Zhou T, Lynch RM, Chen L, Acharya P, Wu X, Doria-Rose NA, Joyce MG, Lingwood D, Soto C, Bailer RT, Ernandes MJ, Kong R, Longo NS, Louder MK, McKee K, O'Dell S, Schmidt SD, Tran L, Yang Z, Druz A, Luongo TS, Moquin S, Srivatsan S, Yang Y, Zhang B, Zheng A, Pancera M, Kirys T, Georgiev IS, Gindin T, Peng HP, Yang AS, Mullikin JC, Gray MD, Stamatatos L, Burton DR, Koff WC, Cohen MS, Haynes BF, Casazza JP, Connors M, Corti D, Lanzavecchia A, Sattentau QJ, Weiss RA, West AP, Bjorkman PJ, Scheid JF, Nussenzweig MC, Shapiro L, Mascola JR, Kwong PD
Cell 161 1280-92 (2015)
PMID: 26004070

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-212608 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Envelope glycoprotein gp160 Chains: E, G
Molecule details ›
Chains: E, G
Length: 354 amino acids
Theoretical weight: 39.67 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8JDI3 (Residues: 43-481; Coverage: 42%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein
8ANC134 Heavy chain Chains: A, H
Molecule details ›
Chains: A, H
Length: 229 amino acids
Theoretical weight: 24.45 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
8ANC134 Light Chain Chains: D, L
Molecule details ›
Chains: D, L
Length: 213 amino acids
Theoretical weight: 23.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NAG 11 x NAG
Ligand SO4 12 x SO4
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: R3
Unit cell:
a: 220.353Å b: 220.353Å c: 118.493Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.208 0.253
Expression system: Homo sapiens

Quick links

Citations

65 review citations

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

2 mentions without citation

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.
Zhou et al. (2015)
1 more