4N5Z

Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/Viet Nam/1203/2004 (H5N1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses.

de Vries, R.P.Zhu, X.McBride, R.Rigter, A.Hanson, A.Zhong, G.Hatta, M.Xu, R.Yu, W.Kawaoka, Y.de Haan, C.A.Wilson, I.A.Paulson, J.C.

(2014) J Virol 88: 768-773

  • DOI: 10.1128/JVI.02690-13
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Two ferret-adapted H5N1 viruses capable of respiratory droplet transmission have been reported with mutations in the hemagglutinin receptor-binding site and stalk domains. Glycan microarray analysis reveals that both viruses exhibit a strong shift to ...

    Two ferret-adapted H5N1 viruses capable of respiratory droplet transmission have been reported with mutations in the hemagglutinin receptor-binding site and stalk domains. Glycan microarray analysis reveals that both viruses exhibit a strong shift toward binding to "human-type" α2-6 sialosides but with notable differences in fine specificity. Crystal structure analysis further shows that the stalk mutation causes no obvious perturbation of the receptor-binding pocket, consistent with its impact on hemagglutinin stability without affecting receptor specificity.


    Organizational Affiliation

    Departments of Cell and Molecular Biology and Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin HA1 chain
A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c
334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 4 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin
B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d
181Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
Find proteins for Q6DQ33 (Influenza A virus)
Go to UniProtKB:  Q6DQ33
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.24α = 88.43
b = 118.943β = 89.68
c = 273.41γ = 60.26
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-10-10 
  • Released Date: 2013-11-20 
  • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-01-01
    Changes: Database references