› 8aed

X-ray diffraction
1.17Å resolution

Broadly neutralizing DARPin bnD.9 in complex with the HIV-1 envelope variable loop 3 peptide V3 (BG505)

Released:
DOI: 10.2210/pdb8aed/pdb
PDB entry 8aed coloured by chain, front view.
PDB entry 8aed coloured by chain, side view.
PDB entry 8aed coloured by chain, top view.
Source organisms:
Primary publication:
Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization.
Glögl M, Friedrich N, Cerutti G, Lemmin T, Kwon YD, Gorman J, Maliqi L, Mittl PRE, Hesselman MC, Schmidt D, Weber J, Foulkes C, Dingens AS, Bylund T, Olia AS, Verardi R, Reinberg T, Baumann NS, Rusert P, Dreier B, Shapiro L, Kwong PD, Plückthun A, Trkola A
Nat Struct Mol Biol (2023)
PMID: 37605043

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-226820 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Broadly neutralizing DARPin bnD.9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 162 amino acids
Theoretical weight: 17.21 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
Surface protein gp120 Chains: C, D
Molecule details ›
Chains: C, D
Length: 24 amino acids
Theoretical weight: 2.57 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: Q9Q714 (Residues: 306-329; Coverage: 3%)
Gene name: env

Ligands and Environments

4 bound ligands:
Ligand EDO 4 x EDO
Ligand ACT 2 x ACT
Ligand MG 3 x MG
Ligand CIT 2 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 50.795Å b: 55.233Å c: 58.032Å
α: 90° β: 98.54° γ: 90°
R-values:
R R work R free
0.156 0.154 0.184
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 citations in other articles

Assessing immunogenicity barriers of the HIV-1 envelope trimer.
Maliqi et al. (2023)