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- EMDB-41826: A mechanistic understanding of protective influenza B neuraminida... -

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Basic information

Entry
Database: EMDB / ID: EMD-41826
TitleA mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Map data
Sample
  • Complex: Complex of human donor mAb-fv domain bound to influenza B neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb-393 heavy chain
    • Protein or peptide: mAb-393 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeuraminidase Sialidase / HYDROLASE
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza B virus (B/Iowa/06/2017)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsFerguson JA / Raghavan SSR / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Immunity / Year: 2024
Title: Isolation of human antibodies against influenza B neuraminidase and mechanisms of protection at the airway interface.
Authors: Rachael M Wolters / James A Ferguson / Ivette A Nuñez / Elaine E Chen / Ty Sornberger / Luke Myers / Svearike Oeverdieck / Sai Sundar Rajan Raghavan / Chandrahaas Kona / Laura S Handal / ...Authors: Rachael M Wolters / James A Ferguson / Ivette A Nuñez / Elaine E Chen / Ty Sornberger / Luke Myers / Svearike Oeverdieck / Sai Sundar Rajan Raghavan / Chandrahaas Kona / Laura S Handal / Trevor E Esilu / Edgar Davidson / Benjamin J Doranz / Taylor B Engdahl / Nurgun Kose / Lauren E Williamson / C Buddy Creech / Katherine N Gibson-Corley / Andrew B Ward / James E Crowe /
Abstract: Influenza B viruses (IBVs) comprise a substantial portion of the circulating seasonal human influenza viruses. Here, we describe the isolation of human monoclonal antibodies (mAbs) that recognized ...Influenza B viruses (IBVs) comprise a substantial portion of the circulating seasonal human influenza viruses. Here, we describe the isolation of human monoclonal antibodies (mAbs) that recognized the IBV neuraminidase (NA) glycoprotein from an individual following seasonal vaccination. Competition-binding experiments suggested the antibodies recognized two major antigenic sites. One group, which included mAb FluB-393, broadly inhibited IBV NA sialidase activity, protected prophylactically in vivo, and bound to the lateral corner of NA. The second group contained an active site mAb, FluB-400, that broadly inhibited IBV NA sialidase activity and virus replication in vitro in primary human respiratory epithelial cell cultures and protected against IBV in vivo when administered systemically or intranasally. Overall, the findings described here shape our mechanistic understanding of the human immune response to the IBV NA glycoprotein through the demonstration of two mAb delivery routes for protection against IBV and the identification of potential IBV therapeutic candidates.
History
DepositionSep 2, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41826.png

Downloads & links

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Map

FileDownload / File: emd_41826.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å		0.73 Å/pix.
x 360 pix.
= 261. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0056260484 - 0.010058191
Average (Standard dev.)0.000003796074 (±0.00034175155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41826_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_41826_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Complex of human donor mAb-fv domain bound to influenza B neurami...

EntireName: Complex of human donor mAb-fv domain bound to influenza B neuraminidase
Components
  • Complex: Complex of human donor mAb-fv domain bound to influenza B neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb-393 heavy chain
    • Protein or peptide: mAb-393 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of human donor mAb-fv domain bound to influenza B neurami...

SupramoleculeName: Complex of human donor mAb-fv domain bound to influenza B neuraminidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (B/Iowa/06/2017)
Molecular weightTheoretical: 51.104258 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTEITAPTM PLDCANASNV QAVNRSATKG VTLLLPGPEW TYPRLSCPG STFQKALLIS PHRFGETKGN SAPLIIREPF VACGPNECKH FALTHYAAQP GGYYNGTRGD RNKLRHLISV K LGKIPTVE ...String:
MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTEITAPTM PLDCANASNV QAVNRSATKG VTLLLPGPEW TYPRLSCPG STFQKALLIS PHRFGETKGN SAPLIIREPF VACGPNECKH FALTHYAAQP GGYYNGTRGD RNKLRHLISV K LGKIPTVE NSIFHMAAWS GSACHDGKEW TYIGVDGPDN NALLKVKYGE AYTDTYHSYA NNILRTQESA CNCIGGNCYL MI TDGSASG VSECRFLKIR EGRIIKEIFP TGRVKHTEEC TCGFASNKTI ECACRDNRYT AKRPFVKLNV ETDTAEIRLM CTD TYLDTP RPNDGSITGP CESDGDKGSG GIKGGFVHQR MKSKIGRWYS RTMSKTERMG MGLYVKYGGD PWADSDALAF SGVM VPMKE PGWYSFGFEI KDKKCDVPCI GIEMVHDGGK ETWHSAATAI YCLMGSGQLL WDTVTGVDMA L

UniProtKB: Neuraminidase

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Macromolecule #2: mAb-393 heavy chain

MacromoleculeName: mAb-393 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.650218 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLQEAGPG LVKPSETLSL TCTVSGGSVS DTSYFWGWIR QPPGKGLEWI GSVSYTGDNY YNPSLRSRVA ISLDAPKNRF SLKLRSVTA ADTAVYYCAR RPTHFDFWKT FDYWGQGSLV TVSS

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Macromolecule #3: mAb-393 light chain

MacromoleculeName: mAb-393 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.812088 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQSIS TWLAWYQQKP GEAPKLLIYK ASNLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYNIYSWTFG QGTKVEIK

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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: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.4 mg/mL
BufferpH: 7.4 / Details: TBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4048 pixel / Digitization - Dimensions - Height: 4048 pixel / Number grids imaged: 1 / Number real images: 6177 / Average electron dose: 49.87 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 190000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, source_name: RoseTTAFold, initial_model_type: in silico model
chain_id: HL, source_name: Other, initial_model_type: in silico modelhttps://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/abodybuilder2_results/20230713_0236990/
Output model

PDB-8u1s:
A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface

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