Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus in complex with Oseltamivir

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

Starting Model: experimental
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A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses.

Escuret, V.Collins, P.J.Casalegno, J.Vachieri, S.G.Cattle, N.Ferraris, O.Sabatier, M.Frobert, E.Caro, V.Skehel, J.J.Gamblin, S.Valla, F.Valette, M.Ottmann, M.Mccauley, J.W.Daniels, R.S.Lina, B.

(2014) J Infect Dis 210: 1260

  • DOI: https://doi.org/10.1093/infdis/jiu244
  • Primary Citation of Related Structures:  
    4CPL, 4CPM, 4CPN, 4CPO, 4CPY, 4CPZ

  • PubMed Abstract: 

    Influenza B viruses with a novel I221L substitution in neuraminidase (NA) conferring high-level resistance to oseltamivir were isolated from an immunocompromised patient after prolonged oseltamivir treatment. Enzymatic characterization of the NAs (Km, Ki) and the in vitro fitness of viruses carrying wild-type or mutated (I221L) NA genes were evaluated. Proportions of wild-type and mutated NA genes were directly quantified in the patient samples. Structural characterizations by X-ray crystallography of a wild-type and I221L variant NA were performed. The Km and Ki revealed that the I221L variant NA had approximately 84 and 51 times lower affinity for oseltamivir carboxylate and zanamivir, respectively, compared with wild-type NA. Viruses with a wild-type or I221L variant NA had similar growth kinetics in Madin-Darby canine kidney (MDCK) cells, and 5 passages in MDCK cells revealed no reversion of the I221L substitution. The crystal structure of the I221L NA and oseltamivir complex showed that the leucine side chain protrudes into the hydrophobic pocket of the active site that accommodates the pentyloxy substituent of oseltamivir. Enzyme kinetic and NA structural analyses provide an explanation for the high level of resistance to oseltamivir while retaining good fitness of viruses carrying I221L variant NA.

  • Organizational Affiliation

    Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
466Influenza B virusMutation(s): 0 
Find proteins for U5XBU0 (Influenza B virus)
Explore U5XBU0 
Go to UniProtKB:  U5XBU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU5XBU0
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
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 
G [auth A],
U [auth B]
(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
C14 H24 N2 O4
Query on NAG

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F [auth A],
T [auth B]
C8 H15 N O6
Query on EDO

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AA [auth B]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
AA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C2 H6 O2
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
G39 BindingDB:  4CPY Ki: 1.1 (nM) from 1 assay(s)
IC50: min: 3, max: 61 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.094α = 90
b = 160.094β = 90
c = 89.8γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2019-10-09
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary