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- EMDB-39606: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-39606
TitleNeuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
Map data
Sample
  • Complex: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
    • Protein or peptide: Vasodilator-stimulated phosphoprotein,Neuraminidase
    • Protein or peptide: CAV-F34 kappa chain
    • Protein or peptide: CAV-F34 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordsinfluenza virus / neuraminidase / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / 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 speciesInfluenza A virus (A/California/04/2009(H1N1)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsWang X / Ge J / Li X
Funding support1 items
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, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39606.png

Downloads & links

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Map

FileDownload / File: emd_39606.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 312 pix.
= 335.15 Å		1.07 Å/pix.
x 312 pix.
= 335.15 Å		1.07 Å/pix.
x 312 pix.
= 335.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.521
Minimum - Maximum-2.907071 - 5.56188
Average (Standard dev.)-0.00052179024 (±0.13207698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 335.15042 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39606_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
Components
  • Complex: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
    • Protein or peptide: Vasodilator-stimulated phosphoprotein,Neuraminidase
    • Protein or peptide: CAV-F34 kappa chain
    • Protein or peptide: CAV-F34 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab

SupramoleculeName: Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))

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Macromolecule #1: Vasodilator-stimulated phosphoprotein,Neuraminidase

MacromoleculeName: Vasodilator-stimulated phosphoprotein,Neuraminidase / type: protein_or_peptide / ID: 1
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).
Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 51.660816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWIFL AAILKGVQCA DPHHHHHHSS SDYSDLQRVK QELLEEVKKE LQKVKEEIIE AFVQELRKRG SLVPRGSGGV KLAGNSSLC PVSGWAIYSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSCP I GEVPSPYN ...String:
MEFGLSWIFL AAILKGVQCA DPHHHHHHSS SDYSDLQRVK QELLEEVKKE LQKVKEEIIE AFVQELRKRG SLVPRGSGGV KLAGNSSLC PVSGWAIYSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSCP I GEVPSPYN SRFESVAWSA SACHDGINWL TIGISGPDSG AVAVLKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTI MT DGPSDGQ ASYKIFRIEK GKIVKSVEMN APNYHYEECS CYPDSSEITC VCRDNWHGSN RPWVSFNQNL EYQIGYICSG VFG DNPRPN DKTGSCGPVS SNGANGVKGF SFKYGNGVWI GRTKSISSRK GFEMIWDPNG WTGTDNNFSI KQDIVGINEW SGYS GSFVQ HPELTGLDCI RPCFWVELIR GRPEENTIWT SGSSISFCGV NSDTVGWSWP DGAELPFTID K

UniProtKB: Vasodilator-stimulated phosphoprotein, Neuraminidase

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Macromolecule #2: CAV-F34 kappa chain

MacromoleculeName: CAV-F34 kappa chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.500826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQYIS SMNLAWYQQK PGQAPRLLIS AASSRATGIP DRFSGSGSGT DFTLTISGLE PEDFAVYYC QKYGSPYTFG QGTKVEIK

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Macromolecule #3: CAV-F34 heavy chain

MacromoleculeName: CAV-F34 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.463903 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVEPGGSLRL SCAASGLTFS TYEMNWVRQA PGKGLEWISH ISSSGFAIYY ADSVRGRFTI SRDIAKQSLD LQMNSLRAE DTAVYYCARD YYNRDLGYSG MDVWGQGTTV TVSS

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 9 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE / Details: alphafold 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242813
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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