› 8fad

Electron Microscopy
4Å resolution

Asymmetric structure of cleaved HIV-1 AD8 envelope glycoprotein trimer in styrene-maleic acid lipid nanoparticles

Released:
DOI: 10.2210/pdb8fad/pdb
PDB entry 8fad coloured by chain, front view.
PDB entry 8fad coloured by chain, side view.
PDB entry 8fad coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles.
Wang K, Zhang S, Go EP, Ding H, Wang WL, Nguyen HT, Kappes JC, Desaire H, Sodroski J, Mao Y
Commun Biol 6 535 (2023)
PMID: 37202420
Related structures: EMD-28953

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-234891 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (9 distinct):
Transmembrane protein gp41 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 138 amino acids
Theoretical weight: 15.67 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A120K6L5 (Residues: 514-651; Coverage: 16%)
Gene name: env
Sequence domains: Retroviral envelope protein
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 469 amino acids
Theoretical weight: 52.78 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: B0FDK7 (Residues: 33-501; Coverage: 92%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
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, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand NAG 22 x NAG
Ligand 83G 3 x 83G
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-28953
Expression system: Homo sapiens

Quick links

Citations

3 citation in other articles

Alterations in gp120 glycans or the gp41 fusion peptide-proximal region modulate the stability of the human immunodeficiency virus (HIV-1) envelope glycoprotein pretriggered conformation.
Zhang et al. (2023)
2 more

1 mention without citation

Alternative substitutions of N332 in HIV-1AD8 gp120 differentially affect envelope glycoprotein function and viral sensitivity to broadly neutralizing antibodies targeting the V3-glycan.
Jeffy et al. (2023)