› 5t3z

X-ray diffraction
3.5Å resolution

3.5 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074

Released:
DOI: 10.2210/pdb5t3z/pdb
PDB entry 5t3z coloured by chain, front view.
PDB entry 5t3z coloured by chain, side view.
PDB entry 5t3z coloured by chain, top view.
Source organisms:
Primary publication:
Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.
Gristick HB, von Boehmer L, West AP, Schamber M, Gazumyan A, Golijanin J, Seaman MS, Fätkenheuer G, Klein F, Nussenzweig MC, Bjorkman PJ
Nat Struct Mol Biol 23 906-915 (2016)
PMID: 27617431

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-558154 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (18 distinct):
Transmembrane protein gp41 Chain: B
Molecule details ›
Chain: B
Length: 153 amino acids
Theoretical weight: 17.15 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 509-661; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 481 amino acids
Theoretical weight: 54.06 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-505, 508-508; Coverage: 56%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
10-1074 Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 238 amino acids
Theoretical weight: 25.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
10-1074 Light Chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
IOMA Heavy Chain Chain: D
Molecule details ›
Chain: D
Length: 232 amino acids
Theoretical weight: 25.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
IOMA Light Chain Chain: E
Molecule details ›
Chain: E
Length: 214 amino acids
Theoretical weight: 22.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN, GAL
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA
Carbohydrate polymer
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: R3
Unit cell:
a: 217.258Å b: 217.258Å c: 154.935Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.278 0.275 0.298
Expression system: Homo sapiens

Quick links

Citations

30 review citations

Recent progress in broadly neutralizing antibodies to HIV.
Sok et al. (2018)
29 more

37 mentions without citation

A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target.
Parker Miller et al. (2021)
36 more