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- EMDB-41824: A mechanistic understanding of protective influenza B neuraminida... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41824
TitleA mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Map data
Sample
  • Complex: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database.
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb-2D10 heavy chain
    • Protein or peptide: mAb-2D10 light chain
KeywordsNeuraminidase Sialidase / HYDROLASE
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 / 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: 3.36 Å
AuthorsFerguson JA / Oeverdieck S / 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: To Be Published
Title: A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Authors: Ferguson JA / Oeverdieck S / Ward AB
History
DepositionSep 1, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41824.png

Downloads & links

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Map

FileDownload / File: emd_41824.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.42
Minimum - Maximum-1.4824197 - 2.715552
Average (Standard dev.)0.000024401517 (±0.05939137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41824_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41824_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database.
Components
  • Complex: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database.
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb-2D10 heavy chain
    • Protein or peptide: mAb-2D10 light chain

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

SupramoleculeName: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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-2D10 heavy chain

MacromoleculeName: mAb-2D10 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.13958 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGDSIS GSSYYWGWIR QPPGKGLEWI GSIYYSGITY YNPSLKSRVT IYVDTSKNQF SLKLNSATA ADTAVYYCAR LYTKSSNANY WGQGTLVTVS S

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Macromolecule #3: mAb-2D10 light chain

MacromoleculeName: mAb-2D10 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.627834 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYD ASSLESGVPS RFSGSGSGTE FTLTISSLQS DDFAIYYCQ QYHSYSGTFG QGTKVEIK

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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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 36000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4048 pixel / Digitization - Dimensions - Height: 4048 pixel / Number grids imaged: 1 / Number real images: 2559 / Average electron dose: 50.43 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 335369

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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-8u1q:
A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface

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