4CPY | pdb_00004cpy

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

• PDB DOI: https://doi.org/10.2210/pdb4CPY/pdb

• Classification: HYDROLASE
• Organism(s): Influenza B virus
• Mutation(s): No 


• Deposited: 2014-02-09 Released: 2014-05-14 
• Deposition Author(s): Vachieri, S.G., Collins, P.J., Escuret, V., Casalegno, J.S., Cattle, N., Ferraris, O., Sabatier, M., Frobert, E., Caro, V., Skehel, J.J., Gamblin, S.J., Valla, F., Valette, M., Ottmann, M., McCauley, J.W., Daniels, R.S., Lina, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.179 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 24795482 
• DOI: https://doi.org/10.1093/infdis/jiu244
• Primary Citation 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.

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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.
Division of Virology.
Division of Virology Division of Molecular Structure.
WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom.
Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and.
Genotyping of Pathogens and Public Health Platform, Institut Pasteur, Paris, France.
Division of Molecular Structure.
Service de Réanimation Pédiatrique, Hôpital Femme Mère Enfant, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron.
Laboratoire de Virologie et Centre National de Référence virus influenzae.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.46 kDa 
• Atom Count: 6,958 
• Modeled Residue Count: 780 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAMINIDASE	A, B	466	Influenza B virus	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for U5XBU0 (Influenza B virus) Explore U5XBU0  Go to UniProtKB:  U5XBU0
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G39	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 NENPYTRHICXVCS-YNEHKIRRSA-N
NAG	F [auth A], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	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]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.179 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.094	α = 90
b = 160.094	β = 90
c = 89.8	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Vachieri, S.G., Collins, P.J., Escuret, V., Casalegno, J.S., Cattle, N., Ferraris, O., Sabatier, M., Frobert, E., Caro, V., Skehel, J.J., Gamblin, S.J., Valla, F., Valette, M., Ottmann, M., McCauley, J.W., Daniels, R.S., Lina, B.

Revision History  

• 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
• Version 2.2: 2024-11-06
  Changes: Structure summary