3ZP3 | pdb_00003zp3

INFLUENZA VIRUS (VN1194) H5 HA A138V mutant with LSTc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.277 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3ZP3

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Changes in the Hemagglutinin of H5N1 Viruses During Human Infection - Influence on Receptor Binding.

Crusat, M.Liu, J.Palma, A.S.Childs, R.A.Liu, Y.Wharton, S.A.Lin, Y.P.Coombs, P.J.Martin, S.R.Matrosovich, M.Chen, Z.Stevens, D.J.Hien, V.M.Thanh, T.T.Nhu, L.N.T.Nguyet, L.A.Ha, D.Q.van Doorn, H.R.Hien, T.T.Conradt, H.S.Kiso, M.Gamblin, S.J.Chai, W.Skehel, J.J.Hay, A.J.Farrar, J.De Jong, M.D.Feizi, T.

(2013) Virology 447: 326

  • DOI: https://doi.org/10.1016/j.virol.2013.08.010
  • Primary Citation Related Structures: 
    3ZP0, 3ZP1, 3ZP2, 3ZP3, 3ZP6, 3ZPA, 3ZPB

  • PubMed Abstract: 

    As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process.


  • Organizational Affiliation
    • Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 57.84 kDa 
  • Atom Count: 3,945 
  • Modeled Residue Count: 479 
  • Deposited Residue Count: 500 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HAEMAGGLUTININA [auth E]340Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 1 
UniProt
Find proteins for Q6DQ34 (Influenza A virus)
Explore Q6DQ34 
Go to UniProtKB:  Q6DQ34
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ34
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HAEMAGGLUTININB [auth F]160Influenza A virus (A/Vietnam/1194/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q6DQ34 (Influenza A virus)
Explore Q6DQ34 
Go to UniProtKB:  Q6DQ34
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ34
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.277 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.07α = 90
b = 101.07β = 90
c = 449.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary