› 6mdt

X-ray diffraction
3.82Å resolution

Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63 space group

Released:
DOI: 10.2210/pdb6mdt/pdb
PDB entry 6mdt coloured by chain, front view.
PDB entry 6mdt coloured by chain, side view.
PDB entry 6mdt coloured by chain, top view.
Source organisms:
Primary publication:
Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide.
Kumar S, Sarkar A, Pugach P, Sanders RW, Moore JP, Ward AB, Wilson IA
OpenAccess logo Nat Commun 10 763 (2019)
PMID: 30770829

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-231595 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (13 distinct):
Transmembrane protein gp41 Chain: B
Molecule details ›
Chain: B
Length: 153 amino acids
Theoretical weight: 17.37 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: B3UES2 (Residues: 516-668; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 482 amino acids
Theoretical weight: 53.98 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: B3UF58 (Residues: 30-511; Coverage: 56%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
35O22 Fab heavy chain Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
35O22 Fab light chain Chain: E
Molecule details ›
Chain: E
Length: 216 amino acids
Theoretical weight: 23.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
PGT124 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 236 amino acids
Theoretical weight: 25.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
PGT124 Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.06 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
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
1 bound ligand:
Ligand NAG 9 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P63
Unit cell:
a: 129.343Å b: 129.343Å c: 313.071Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.295 0.294 0.311
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Strategies for inducing effective neutralizing antibody responses against HIV-1.
Del Moral-Sánchez et al. (2019)
1 more

2 mentions without citation

Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.
Henderson et al. (2020)
1 more