› 6ck9

X-ray diffraction
2.71Å resolution

Crystal Structure of HIV-1 ConC_Base0 Prefusion Env Trimer in Complex with Human Antibody Fragment 3H109L and 35O22 variants at 3.5 Angstrom

Released:
DOI: 10.2210/pdb6ck9/pdb
PDB entry 6ck9 coloured by chain, front view.
PDB entry 6ck9 coloured by chain, side view.
PDB entry 6ck9 coloured by chain, top view.
Source organisms:
Primary publication:
A Universal Approach to Optimize the Folding and Stability of Prefusion-Closed HIV-1 Envelope Trimers.
Rutten L, Lai YT, Blokland S, Truan D, Bisschop IJM, Strokappe NM, Koornneef A, van Manen D, Chuang GY, Farney SK, Schuitemaker H, Kwong PD, Langedijk JPM
Cell Rep 23 584-595 (2018)
PMID: 29642014

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-513699 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (12 distinct):
Transmembrane protein gp41 Chain: B
Molecule details ›
Chain: B
Length: 153 amino acids
Theoretical weight: 17.25 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: E9MY73 (Residues: 511-663; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
35O22 scFv heavy chain portion Chain: D
Molecule details ›
Chain: D
Length: 134 amino acids
Theoretical weight: 14.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
35O22 scFv light chain portion Chain: E
Molecule details ›
Chain: E
Length: 114 amino acids
Theoretical weight: 12.36 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 463 amino acids
Theoretical weight: 52.68 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: E1ADR9 (Residues: 32-499; Coverage: 54%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
3H109L Fab heavy chain Chain: H
Molecule details ›
Chain: H
Length: 244 amino acids
Theoretical weight: 26.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
3H109L Fab light chain Chain: L
Molecule details ›
Chain: L
Length: 217 amino acids
Theoretical weight: 23.42 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, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
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: APS BEAMLINE 22-ID
Spacegroup: P63
Unit cell:
a: 131.9Å b: 131.9Å c: 314.86Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.25 0.248 0.288
Expression system: Homo sapiens

Quick links

Citations

14 review citations

Protein and Glycan Mimicry in HIV Vaccine Design.
Seabright et al. (2019)
13 more

10 mentions without citation

Stabilisation of Viral Membrane Fusion Proteins in Prefusion Conformation by Structure-Based Design for Structure Determination and Vaccine Development.
Ebel et al. (2022)
9 more