› 6nm6

X-ray diffraction
2.74Å resolution

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to N6 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.2 Angstrom

Released:
DOI: 10.2210/pdb6nm6/pdb
Model geometry
Fit model/data
PDB entry 6nm6 coloured by chain, front view.
PDB entry 6nm6 coloured by chain, side view.
PDB entry 6nm6 coloured by chain, top view.
Source organisms:
Primary publication:
Improvement of antibody functionality by structure-guided paratope engraftment.
Liu Q, Lai YT, Zhang P, Louder MK, Pegu A, Rawi R, Asokan M, Chen X, Shen CH, Chuang GY, Yang ES, Miao H, Wang Y, Fauci AS, Kwong PD, Mascola JR, Lusso P
OpenAccess logo Nat Commun 10 721 (2019)
PMID: 30760721

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212148 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (13 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
35O22 scFv heavy chain Chain: D
Molecule details ›
Chain: D
Length: 153 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
35O22 scFv light chain Chain: E
Envelope glycoprotein gp160 Chain: G
3H109L Fab heavy chain Chain: H
3H109L Fab light chain Chain: L
N6 FR3-03 heavy chain Chain: U
N6 FR3-03 light chain Chain: V

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
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 7 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P63
Unit cell:
a: 128.24Å b: 128.24Å c: 315.77Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.242 0.24 0.288
Expression system: Homo sapiens

Quick links

Citations

5 review citations

Application of CRISPR/Cas9-Based Gene Editing in HIV-1/AIDS Therapy.
Xiao et al. (2019)
4 more

4 mentions without citation

Quaternary Interaction of the HIV-1 Envelope Trimer with CD4 and Neutralizing Antibodies.
Liu et al. (2021)
3 more