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- EMDB-29704: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FN... -

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Basic information

Entry
Database: EMDB / ID: EMD-29704
TitleN2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FNI9 Fab molecules
Map data
Sample
  • Complex: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FNI9 Fab molecules
    • Protein or peptide: Neuraminidase
    • Protein or peptide: FNI9 Fab heavy chain
    • Protein or peptide: FNI9 Fab light chain
  • Ligand: CALCIUM IONCalcium
Keywordsviral glycoprotein / antibody / Fab / influenza / virus / 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: 3.0 Å
AuthorsDang HV / Snell G
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
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_29704.png

Downloads & links

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Map

FileDownload / File: emd_29704.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.093 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.020519191 - 0.05041214
Average (Standard dev.)0.0000073275073 (±0.0009643826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions402402402
Spacing402402402
CellA=B=C: 439.38602 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_29704_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29704_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29704_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FN...

EntireName: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FNI9 Fab molecules
Components
  • Complex: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FNI9 Fab molecules
    • Protein or peptide: Neuraminidase
    • Protein or peptide: FNI9 Fab heavy chain
    • Protein or peptide: FNI9 Fab light chain
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FN...

SupramoleculeName: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 3 FNI9 Fab molecules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment generated by proteolytic cleavage of FNI9 IgG1 antibody
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 0.42 kDa/nm

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Details: A/Tanzania/205/2010 H3N2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 54.755047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGENL YFQGSAEYRN WSKPQCDITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDP DKCYQFALGQ G TTLNNVHS ...String:
METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGENL YFQGSAEYRN WSKPQCDITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDP DKCYQFALGQ G TTLNNVHS NNTVRDRTPY RTLLMNELGV PFHLGTKQVC IAWSSSSCHD GKAWLHVCIT GDDKNATASF IYNGRLVDSV VS WSKEILR TQESECVCIN GTCTVVMTDG SASGKADTKI LFIEEGKIVH TSTLSGSAQH VEECSCYPRY PGVRCVCRDN WKG SNRPIV DINIKDHSIV SSYVCSGLVG DTPRKNDSSS SSHCLDPNNE EGGHGVKGWA FDDGNDVWMG RTINETSRLG YETF KVIEG WSNPKSKLQI NRQVIVDRGN RSGYSGIFSV EGKSCINRCF YVELIRGRKE ETEVLWTSNS IVVFCGTSGT YGTGS WPDG ADLNLMPI

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Macromolecule #2: FNI9 Fab heavy chain

MacromoleculeName: FNI9 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.418053 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVHLVQSGAE VKEPGSSVTV SCKASGGSFN NQAISWVRQA PGQGLEWMGG IFPISGTPTS AQRFQGRVTF TADESTTTVY MDLSSLRSD DTAVYYCARA GSDYFNRDLG WENYYFASWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVHLVQSGAE VKEPGSSVTV SCKASGGSFN NQAISWVRQA PGQGLEWMGG IFPISGTPTS AQRFQGRVTF TADESTTTVY MDLSSLRSD DTAVYYCARA GSDYFNRDLG WENYYFASWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSC

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Macromolecule #3: FNI9 Fab light chain

MacromoleculeName: FNI9 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.565068 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVMTQSPAT LSLSSGERAT LSCRASRSVS SNLAWYQQKP GQAPRLLIYD ASTRATGFSA RFAGSGSGTE FTLTISSLQS EDSAIYYCQ QYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSLSSGERAT LSCRASRSVS SNLAWYQQKP GQAPRLLIYD ASTRATGFSA RFAGSGSGTE FTLTISSLQS EDSAIYYCQ QYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / 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

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
50.0 mMC4H11NO3Tris
10.0 mMCaCl2calcium chloride

Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
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: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217552

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