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 

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This is version 2.0 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
  • Primary Citation of Related Structures:  
    4N5Y, 4N5Z

  • 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 toward binding to "human-type" α2-6 sialosides but with notable differences in fine specificity ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain334Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 4 
Gene Names: HA
UniProt
Find proteins for Q5EP31 (Influenza A virus)
Explore Q5EP31 
Go to UniProtKB:  Q5EP31
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin181Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus)
Explore Q6DQ33 
Go to UniProtKB:  Q6DQ33
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], NA [auth n], OA [auth o], PA [auth p]
EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], NA [auth n], OA [auth o], PA [auth p], RA [auth r], TA [auth t], VA [auth v], XA [auth x]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0], FA [auth f], IA [auth i], KA [auth k], MA [auth m], QA [auth q], SA [auth s], UA [auth u]
AB [auth 0], FA [auth f], IA [auth i], KA [auth k], MA [auth m], QA [auth q], SA [auth s], UA [auth u], WA [auth w], YA [auth y], ZA [auth z]
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-01-01
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary