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- PDB-8yvl: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab -

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Basic information

Entry
Database: PDB / ID: 8yvl
TitleNeuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
Components
  • CAV-F34 heavy chain
  • CAV-F34 kappa chain
  • Vasodilator-stimulated phosphoprotein,Neuraminidase
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza virus / neuraminidase / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / exo-alpha-sialidase / exo-alpha-sialidase activity / lamellipodium membrane / Generation of second messenger molecules ...profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / exo-alpha-sialidase / exo-alpha-sialidase activity / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / axon guidance / viral budding from plasma membrane / neural tube closure / SH3 domain binding / actin cytoskeleton / actin binding / protein homotetramerization / carbohydrate metabolic process / postsynapse / cadherin binding / focal adhesion / host cell plasma membrane / virion membrane / glutamatergic synapse / extracellular exosome / metal ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 ...Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Neuraminidase / Vasodilator-stimulated phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsWang, X. / Ge, J. / Li, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
Authors: Wang, X. / Ge, J. / Li, X.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 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: Vasodilator-stimulated phosphoprotein,Neuraminidase
B: Vasodilator-stimulated phosphoprotein,Neuraminidase
C: Vasodilator-stimulated phosphoprotein,Neuraminidase
D: Vasodilator-stimulated phosphoprotein,Neuraminidase
E: CAV-F34 kappa chain
F: CAV-F34 kappa chain
G: CAV-F34 kappa chain
H: CAV-F34 kappa chain
I: CAV-F34 heavy chain
J: CAV-F34 heavy chain
K: CAV-F34 heavy chain
L: CAV-F34 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,51733
Polymers306,50212
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
Vasodilator-stimulated phosphoprotein,Neuraminidase / VASP


Mass: 51660.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Influenza A virus (A/California/04/2009(H1N1) (TAX ID 641501) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID TR: ...Details: Sequence reference for Influenza A virus (A/California/04/2009(H1N1) (TAX ID 641501) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID TR:A0A2R4G842 with TAX ID 11320 (Influenza A virus).
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: VASP, NA / Production host: Homo sapiens (human)
References: UniProt: P50552, UniProt: A0A2R4G842, exo-alpha-sialidase
#2: Antibody
CAV-F34 kappa chain


Mass: 11500.826 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
CAV-F34 heavy chain


Mass: 13463.903 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 / Feature type: SUBJECT OF INVESTIGATION
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 / Feature type: SUBJECT OF INVESTIGATION
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: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242813 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00619460
ELECTRON MICROSCOPYf_angle_d0.69926412
ELECTRON MICROSCOPYf_dihedral_angle_d6.6862680
ELECTRON MICROSCOPYf_chiral_restr0.0522796
ELECTRON MICROSCOPYf_plane_restr0.0053432

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