H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

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H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant Explained by Kinetic and Structural Analysis

Van Der Vries, E.Collins, P.J.Vachieri, S.G.Xiong, X.Liu, J.Walker, P.A.Haire, L.F.Hay, A.J.Schutten, M.Osterhaus, A.D.M.E.Martin, S.R.Boucher, C.A.B.Skehel, J.J.Gamblin, S.J.

(2012) PLoS Pathog 8: 2914

  • DOI: https://doi.org/10.1371/journal.ppat.1002914
  • Primary Citation of Related Structures:  
    4B7J, 4B7M, 4B7N, 4B7Q, 4B7R

  • PubMed Abstract: 

    Two classes of antiviral drugs, neuraminidase inhibitors and adamantanes, are approved for prophylaxis and therapy against influenza virus infections. A major concern is that antiviral resistant viruses emerge and spread in the human population. The 2009 pandemic H1N1 virus is already resistant to adamantanes. Recently, a novel neuraminidase inhibitor resistance mutation I223R was identified in the neuraminidase of this subtype. To understand the resistance mechanism of this mutation, the enzymatic properties of the I223R mutant, together with the most frequently observed resistance mutation, H275Y, and the double mutant I223R/H275Y were compared. Relative to wild type, K(M) values for MUNANA increased only 2-fold for the single I223R mutant and up to 8-fold for the double mutant. Oseltamivir inhibition constants (K(I)) increased 48-fold in the single I223R mutant and 7500-fold in the double mutant. In both cases the change was largely accounted for by an increased dissociation rate constant for oseltamivir, but the inhibition constants for zanamivir were less increased. We have used X-ray crystallography to better understand the effect of mutation I223R on drug binding. We find that there is shrinkage of a hydrophobic pocket in the active site as a result of the I223R change. Furthermore, R223 interacts with S247 which changes the rotamer it adopts and, consequently, binding of the pentoxyl substituent of oseltamivir is not as favorable as in the wild type. However, the polar glycerol substituent present in zanamivir, which mimics the natural substrate, is accommodated in the I223R mutant structure in a similar way to wild type, thus explaining the kinetic data. Our structural data also show that, in contrast to a recently reported structure, the active site of 2009 pandemic neuraminidase can adopt an open conformation.

  • Organizational Affiliation

    Erasmus Medical Centre, Department of Virology, Rotterdam, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
387Influenza A virus (A/California/07/2009(H1N1))Mutation(s): 1 
Find proteins for C7FH46 (Influenza A virus)
Explore C7FH46 
Go to UniProtKB:  C7FH46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7FH46
Glycosylation Sites: 3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G39

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

Download Ideal Coordinates CCD File 
DA [auth D],
I [auth A],
O [auth B],
V [auth C]
C8 H18 N2 O4 S
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
GA [auth D]
J [auth A]
K [auth A]
EA [auth D],
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
C8 H15 N O6
Query on CA

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
L [auth B]
AA [auth D],
BA [auth D],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
S [auth C],
T [auth C]
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 BindingDB:  4B7R Ki: min: 0.1, max: 10 (nM) from 5 assay(s)
IC50: min: 0.1, max: 210 (nM) from 20 assay(s)
PDBBind:  4B7R Ki: 0.23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.65α = 90
b = 148.82β = 90
c = 166.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2013-07-17
    Changes: Atomic model, Derived calculations, Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary