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- PDB-9nj2: N1 neuraminidase of influenza A/Vietnam/1203/2004 H5N1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9nj2
TitleN1 neuraminidase of influenza A/Vietnam/1203/2004 H5N1 in complex with four FNI9 Fab molecules
Components
  • FNI9 Fab heavy chain
  • FNI9 Fab light chain
  • Neuraminidase
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / neuraminidase / N1 / H5N1 / influenza / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / identical protein binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsErrico, J.M. / Dang, H.V. / Snell, G.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22fk0108141 Japan
Japan Agency for Medical Research and Development (AMED)JP243fa627005 Japan
Japan Agency for Medical Research and Development (AMED)JP243fa727002 Japan
CitationJournal: To Be Published
Title: Potent efficacy of a NA-targeting antibody against a broad spectrum of H5N1 influenza viruses
Authors: Moriyama, S. / Di Iulio, J. / Zatta, F. / Hauser, K. / Asanuma, H. / Munoz, H.E. / Errico, J.M. / Adachi, Y. / Dang, H.V. / Czudnochowski, N. / Sasaki, E. / Chen, A. / Chen, Y. / Kotaki, R. ...Authors: Moriyama, S. / Di Iulio, J. / Zatta, F. / Hauser, K. / Asanuma, H. / Munoz, H.E. / Errico, J.M. / Adachi, Y. / Dang, H.V. / Czudnochowski, N. / Sasaki, E. / Chen, A. / Chen, Y. / Kotaki, R. / Peter, A. / Vetti, E. / Onodera, T. / Maher, M.C. / Rosen, L.E. / Shirakura, M. / Snell, G. / Hasegawa, H. / Takahashi, Y. / Corti, D. / Pizzuto, M.S.
History
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data 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
H: FNI9 Fab heavy chain
I: FNI9 Fab heavy chain
J: FNI9 Fab heavy chain
K: FNI9 Fab heavy chain
L: FNI9 Fab light chain
M: FNI9 Fab light chain
N: FNI9 Fab light chain
O: FNI9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,71433
Polymers309,69912
Non-polymers3,01521
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Neuraminidase


Mass: 51769.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Vietnam/1203/2004 H5N1 / Gene: NA / Production host: Homo sapiens (human) / References: UniProt: Q6DPL2, exo-alpha-sialidase
#2: Antibody
FNI9 Fab heavy chain


Mass: 13850.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
FNI9 Fab light chain


Mass: 11805.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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.: 12 / 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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in complex with FNI9 FabCOMPLEX#1-#30MULTIPLE SOURCES
2N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1)COMPLEX#11RECOMBINANT
3FNI9 FabCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Influenza A virus (A/Viet Nam/1203/2004(H5N1))284218
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 47.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166858 / Symmetry type: POINT
RefinementResolution: 2.4→165.42 Å / Cor.coef. Fo:Fc: 0.726 / SU B: 7.023 / SU ML: 0.152 / ESU R: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.37424 --
obs0.37424 434563 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 46.18 Å2
Refinement stepCycle: 1 / Total: 19073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01219612
ELECTRON MICROSCOPYr_bond_other_d00.01617328
ELECTRON MICROSCOPYr_angle_refined_deg1.661.77726708
ELECTRON MICROSCOPYr_angle_other_deg0.9351.74240032
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.83552444
ELECTRON MICROSCOPYr_dihedral_angle_2_deg13.8225112
ELECTRON MICROSCOPYr_dihedral_angle_3_deg10.846102952
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1350.22860
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0223696
ELECTRON MICROSCOPYr_gen_planes_other0.0020.024776
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.0084.3759824
ELECTRON MICROSCOPYr_mcbond_other3.0074.3759824
ELECTRON MICROSCOPYr_mcangle_it4.9897.83812252
ELECTRON MICROSCOPYr_mcangle_other4.9897.83912253
ELECTRON MICROSCOPYr_scbond_it4.3234.8379788
ELECTRON MICROSCOPYr_scbond_other4.3234.8389789
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.3228.6314457
ELECTRON MICROSCOPYr_long_range_B_refined11.90352.4182024
ELECTRON MICROSCOPYr_long_range_B_other11.90352.4182025
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.755 32189 -
obs--100 %

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