› 6b0n

X-ray diffraction
3.4Å resolution

Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of the clade A BG505 isolate (NFL construct) in complex with Fabs PGT122 and PGV19 at 3.39 A

Released:
DOI: 10.2210/pdb6b0n/pdb
PDB entry 6b0n coloured by chain, front view.
PDB entry 6b0n coloured by chain, side view.
PDB entry 6b0n coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.
Sarkar A, Bale S, Behrens AJ, Kumar S, Sharma SK, de Val N, Pallesen J, Irimia A, Diwanji DC, Stanfield RL, Ward AB, Crispin M, Wyatt RT, Wilson IA
OpenAccess logo Nat Commun 9 1956 (2018)
PMID: 29769533

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-558240 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (15 distinct):
PGV19 Fab heavy chain Chain: D
Molecule details ›
Chain: D
Length: 223 amino acids
Theoretical weight: 24.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
PGV19 light chain Chain: E
Molecule details ›
Chain: E
Length: 209 amino acids
Theoretical weight: 22.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 638 amino acids
Theoretical weight: 70.85 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-503, 509-661; Coverage: 73%)
Gene name: env
Sequence domains:
PGT122 Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 25.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
PGT122 light chain Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 22.88 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: MAN, BMA
Carbohydrate polymer
2 bound ligands:
Ligand NAG 12 x NAG
Ligand MAN 2 x MAN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P63
Unit cell:
a: 161.247Å b: 161.247Å c: 245.651Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.336 0.335 0.346
Expression system: Homo sapiens

Quick links

Citations

11 review citations

The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases.
Izaguirre G. (2019)
10 more

10 mentions without citation

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