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- EMDB-29710: N2 neuraminidase of A/Hong_Kong/2671/2019 in complex with 4 FNI19... -

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Basic information

Entry
Database: EMDB / ID: EMD-29710
TitleN2 neuraminidase of A/Hong_Kong/2671/2019 in complex with 4 FNI19 Fab molecules
Map data
Sample
  • Complex: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong_Kong/2671/2019 strain
    • Protein or peptide: Neuraminidase
    • Protein or peptide: FNI19 Fab heavy chain
    • Protein or peptide: FNI19 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
Keywordsviral glycoprotein / antibody / Fab / influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDang HV / Snell G
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2023
Title: A pan-influenza antibody inhibiting neuraminidase via receptor mimicry.
Authors: Corey Momont / Ha V Dang / Fabrizia Zatta / Kevin Hauser / Caihong Wang / Julia di Iulio / Andrea Minola / Nadine Czudnochowski / Anna De Marco / Kaitlin Branch / David Donermeyer / Siddhant ...Authors: Corey Momont / Ha V Dang / Fabrizia Zatta / Kevin Hauser / Caihong Wang / Julia di Iulio / Andrea Minola / Nadine Czudnochowski / Anna De Marco / Kaitlin Branch / David Donermeyer / Siddhant Vyas / Alex Chen / Elena Ferri / Barbara Guarino / Abigail E Powell / Roberto Spreafico / Samantha S Yim / Dale R Balce / Istvan Bartha / Marcel Meury / Tristan I Croll / David M Belnap / Michael A Schmid / William Timothy Schaiff / Jessica L Miller / Elisabetta Cameroni / Amalio Telenti / Herbert W Virgin / Laura E Rosen / Lisa A Purcell / Antonio Lanzavecchia / Gyorgy Snell / Davide Corti / Matteo Samuele Pizzuto /
Abstract: Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies ...Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift and suboptimal immune responses. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
History
DepositionFeb 8, 2023-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29710.png

Downloads & links

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Map

FileDownload / File: emd_29710.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.97594917 - 2.1584377
Average (Standard dev.)-0.0002992226 (±0.048177052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29710_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_29710_additional_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_29710_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29710_half_map_2.map
Projections & Slices
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Sample components

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Entire : 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong...

EntireName: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong_Kong/2671/2019 strain
Components
  • Complex: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong_Kong/2671/2019 strain
    • Protein or peptide: Neuraminidase
    • Protein or peptide: FNI19 Fab heavy chain
    • Protein or peptide: FNI19 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong...

SupramoleculeName: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong_Kong/2671/2019 strain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment generated by proteolytic cleavage of FNI19 IgG1 antibody
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Details: A/Hong_Kong/2671/2019 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 54.570906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGLVP RGSGSAEYRN WSKPQCGITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDL DKCYQFALGQ G TTLNNVHS ...String:
METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGLVP RGSGSAEYRN WSKPQCGITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDL DKCYQFALGQ G TTLNNVHS NNTVRDRTPY RTLLMNELGV PFHLGTKQVC IAWSSSSCHD GKAWLHVCIT GDDKNATASF IYNGRLVDSV VS WSNDILR TQESECVCIN GTCTVVMTDG NATGKADTKI LFIEEGKIVH TSKLSGSAQH VEECSCYPRY PGVRCVCRDN WKG SNRPII DINIKDHSIV SSYVCSGLVG DTPRKSDSSS SSHCLNPNNE EGGHGVKGWA FDDGNDVWMG RTINETSRLG YETF KVVEG WSNPKSKLQI NRQVIVDRGD RSGYSGIFSV EGKSCINRCF YVELIRGRKE ETEVLWTSNS IVVFCGTSGT YGTGS WPDG ADLNLMHT

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Macromolecule #2: FNI19 Fab heavy chain

MacromoleculeName: FNI19 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.692602 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKRPGSSVRV SCKASEGTFN KYTLTWVRQA PGQGLEWMGG IIPISGIANY AQKFQGRVAI TADESTTTAY MELSSLRSE DSAVYYCATA VSDYFNRDLG WEDYYFPFWG QGTLVTVASA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE VKRPGSSVRV SCKASEGTFN KYTLTWVRQA PGQGLEWMGG IIPISGIANY AQKFQGRVAI TADESTTTAY MELSSLRSE DSAVYYCATA VSDYFNRDLG WEDYYFPFWG QGTLVTVASA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSC

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Macromolecule #3: FNI19 Fab light chain

MacromoleculeName: FNI19 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.549264 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVMTQSPAT LSVSPGARAT LFCRASRSVS DNLAWYQQKP GQAPRLLIFG ASTRATGVPA RFSGSGSGTQ FTLTISSLQS EDFAVYYCQ HYNIWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSVSPGARAT LFCRASRSVS DNLAWYQQKP GQAPRLLIFG ASTRATGVPA RFSGSGSGTQ FTLTISSLQS EDFAVYYCQ HYNIWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / 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

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloridesodium chloride
10.0 mMCaCl2calcium chloride

Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.61 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 885566

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