› 3znl

X-ray diffraction
2.5Å resolution

H5 Haemagglutinin in Complex with 6-O-Sulfo-Sialyl-Lewis X (Sulfated Lewis X)

Released:
DOI: 10.2210/pdb3znl/pdb
PDB entry 3znl coloured by chain, front view.
PDB entry 3znl coloured by chain, side view.
PDB entry 3znl coloured by chain, top view.
Source organism: Influenza A virus (A/Vietnam/1194/2004(H5N1))
Primary publication:
Recognition of sulphated and fucosylated receptor sialosides by A/Vietnam/1194/2004 (H5N1) influenza virus.
Xiong X, Tuzikov A, Coombs PJ, Martin SR, Walker PA, Gamblin SJ, Bovin N, Skehel JJ
Virus Res 178 12-4 (2013)
PMID: 24036174

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179550 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Hemagglutinin Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 326 amino acids
Theoretical weight: 36.95 KDa
Source organism: Influenza A virus (A/Vietnam/1194/2004(H5N1))
UniProt:
  • Canonical: Q6DQ34 (Residues: 17-342; Coverage: 58%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains:
Hemagglutinin Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 166 amino acids
Theoretical weight: 19.1 KDa
Source organism: Influenza A virus (A/Vietnam/1194/2004(H5N1))
UniProt:
  • Canonical: Q6DQ34 (Residues: 347-512; Coverage: 29%)
Gene name: HA
Sequence domains: Haemagglutinin
Structure domains: Hemagglutinin Ectodomain; Chain B

Ligands and Environments

Carbohydrate polymer : NEW Components: NGS, GLA, SIA, FUC
Carbohydrate polymer
2 bound ligands:
Ligand NAG 9 x NAG
Ligand EPE 3 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 175.98Å b: 101.6Å c: 161.37Å
α: 90° β: 111.32° γ: 90°
R-values:
R R work R free
0.238 0.237 0.256

Quick links

Citations

3 review citations

Structural biology of antibody recognition of carbohydrate epitopes and potential uses for targeted cancer immunotherapies.
Dingjan et al. (2015)
2 more

1 mention without citation

HA-Dependent Tropism of H5N1 and H7N9 Influenza Viruses to Human Endothelial Cells Is Determined by Reduced Stability of the HA, Which Allows the Virus To Cope with Inefficient Endosomal Acidification and Constitutively Expressed IFITM3.
Hensen et al. (2019)