› 3r2x

X-ray diffraction
3.1Å resolution

Crystal structure of the de novo designed binding protein HB36.3 in complex the the 1918 influenza virus hemagglutinin

Released:
DOI: 10.2210/pdb3r2x/pdb
PDB entry 3r2x coloured by chain, front view.
PDB entry 3r2x coloured by chain, side view.
PDB entry 3r2x coloured by chain, top view.
Source organisms:
Primary publication:
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.
Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D
Science 332 816-21 (2011)
PMID: 21566186

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163961 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Hemagglutinin HA1 chain Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 36.45 KDa
Source organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9WFX3 (Residues: 18-344; Coverage: 60%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains:
Hemagglutinin HA2 chain Chain: B
Molecule details ›
Chain: B
Length: 179 amino acids
Theoretical weight: 20.39 KDa
Source organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9WFX3 (Residues: 345-520; Coverage: 32%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin Ectodomain; Chain B
HB36.3, designed hemagglutinin binding protein Chain: C
Molecule details ›
Chain: C
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21(DE3)
Structure domains: Apc36109-like domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: R32
Unit cell:
a: 130.054Å b: 130.054Å c: 313.735Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.223 0.249
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

85 review citations

The protein-folding problem, 50 years on.
Dill et al. (2012)
84 more

21 mentions without citation

Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses.
Burton et al. (2012)
20 more