4WA4

The crystal structure of neuraminidase from a H3N8 influenza virus isolated from New England harbor seals in complex with oseltamivir carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals.

Yang, H.Nguyen, H.T.Carney, P.J.Guo, Z.Chang, J.C.Jones, J.Davis, C.T.Villanueva, J.M.Gubareva, L.V.Stevens, J.

(2015) J Virol 89: 2801-2812

  • DOI: 10.1128/JVI.02723-14
  • Primary Citation of Related Structures:  
    4WA1, 4WA2, 4WA3, 4WA4, 4WA5

  • PubMed Abstract: 
  • In late 2011, an A(H3N8) influenza virus infection resulted in the deaths of 162 New England harbor seals. Virus sequence analysis and virus receptor binding studies highlighted potential markers responsible for mammalian adaptation and a mixed receptor binding preference (S ...

    In late 2011, an A(H3N8) influenza virus infection resulted in the deaths of 162 New England harbor seals. Virus sequence analysis and virus receptor binding studies highlighted potential markers responsible for mammalian adaptation and a mixed receptor binding preference (S. J. Anthony, J. A. St Leger, K. Pugliares, H. S. Ip, J. M. Chan, Z. W. Carpenter, I. Navarrete-Macias, M. Sanchez-Leon, J. T. Saliki, J. Pedersen, W. Karesh, P. Daszak, R. Rabadan, T. Rowles, W. I. Lipkin, MBio 3:e00166-00112, 2012, http://dx.doi.org/10.1128/mBio.00166-12). Here, we present a detailed structural and biochemical analysis of the surface antigens of the virus. Results obtained with recombinant proteins for both the hemagglutinin and neuraminidase indicate a true avian receptor binding preference. Although the detection of this virus in new species highlights an increased potential for cross-species transmission, our results indicate that the A(H3N8) virus currently poses a low risk to humans.


    Organizational Affiliation

    Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA fwb4@cdc.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NeuraminidaseA388Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for I6NW33 (Influenza A virus)
Explore I6NW33 
Go to UniProtKB:  I6NW33
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G39 (Subject of Investigation/LOI)
Query on G39

Download Ideal Coordinates CCD File 
C [auth A](3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
NENPYTRHICXVCS-YNEHKIRRSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 Binding MOAD:  4WA4 IC50: 0.66 (nM) from 1 assay(s)
BindingDB:  4WA4 IC50: 8.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.666α = 90
b = 90.666β = 90
c = 108.354γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary