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- PDB-9hli: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor -

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Basic information

Entry
Database: PDB / ID: 9hli
TitleInfluenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / Influenza / Neuraminidase
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsMoran, E. / Davies, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Oseltamivir aziridines are neuraminidase imaging agents and potent anti-influenza agents
Authors: Moran, E. / Vriends, M. / Calvelo, M. / Hansen, T. / Pickles, I. / Xin, X. / Biezeno, M. / Armstrong, Z. / Ferras, M. / Li, L. / Lilley, A. / Harvey, R. / Schroder, S. / Van der Marel, G. / ...Authors: Moran, E. / Vriends, M. / Calvelo, M. / Hansen, T. / Pickles, I. / Xin, X. / Biezeno, M. / Armstrong, Z. / Ferras, M. / Li, L. / Lilley, A. / Harvey, R. / Schroder, S. / Van der Marel, G. / Artola, M. / Aerts, J. / Blaza, J. / Rovira, C. / Codee, J. / Overkleeft, H. / Davies, G.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,52116
Polymers169,9984
Non-polymers2,52312
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Neuraminidase


Mass: 42499.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7FH46, exo-alpha-sialidase
#2: Chemical
ChemComp-A1IVX / (3~{S},4~{R},5~{R},6~{R})-4-acetamido-3-azanyl-6-(butanoylamino)-5-pentan-3-yloxy-cyclohexene-1-carboxylic acid


Mass: 369.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7 / Details: 25 mM Tris pH 7.0 150 mM NaCl, 100 mM CaCl2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisTris1
2150 mMSodium chlorideNaCl1
3100 mMCalcium chlorideCaCl21
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot force -10 and blot time 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 43.99 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFINDCTF correction
7Coot0.9.8.92model fitting
9PHENIX1.21.1_5286:model refinement
10RELIONinitial Euler assignment
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216385 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311792
ELECTRON MICROSCOPYf_angle_d0.64616032
ELECTRON MICROSCOPYf_dihedral_angle_d6.7811724
ELECTRON MICROSCOPYf_chiral_restr0.0521704
ELECTRON MICROSCOPYf_plane_restr0.0052080

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