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- PDB-8u1q: A mechanistic understanding of protective influenza B neuraminida... -

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Basic information

Entry
Database: PDB / ID: 8u1q
TitleA mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface
Components
  • Neuraminidase
  • mAb-2D10 heavy chain
  • mAb-2D10 light chain
KeywordsHYDROLASE / Neuraminidase Sialidase
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 speciesInfluenza B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsFerguson, J.A. / Oeverdieck, S. / Ward, A.B.
Funding support United States, 1items
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, J.A. / Oeverdieck, S. / Ward, A.B.
History
DepositionSep 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
H: mAb-2D10 heavy chain
L: mAb-2D10 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2964
Polymers75,8723
Non-polymers4241
Water0
1
A: Neuraminidase
H: mAb-2D10 heavy chain
L: mAb-2D10 light chain
hetero molecules

A: Neuraminidase
H: mAb-2D10 heavy chain
L: mAb-2D10 light chain
hetero molecules

A: Neuraminidase
H: mAb-2D10 heavy chain
L: mAb-2D10 light chain
hetero molecules

A: Neuraminidase
H: mAb-2D10 heavy chain
L: mAb-2D10 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,18416
Polymers303,48712
Non-polymers1,6984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C4 (4 fold cyclic))

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Components

#1: Protein Neuraminidase /


Mass: 51104.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Iowa/06/2017) / Gene: NA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): D2 / References: UniProt: A0A1S7DL21
#2: Antibody mAb-2D10 heavy chain


Mass: 13139.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody mAb-2D10 light chain


Mass: 11627.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of human mAb-fv domain bound to influenza B neuraminidase, from a public database.
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Drosophila melanogaster (fruit fly)7227D2pCoBlast
31Cricetulus griseus (Chinese hamster)10029ExpiCHO
Buffer solutionpH: 7.4 / Details: TBS
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Calibrated magnification: 36000 X / Nominal defocus max: 700 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 50.43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2559
Image scansWidth: 4048 / Height: 4048

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Processing

EM software
IDNameCategoryDetails
1cryoSPARCparticle selectionTemplate Picker
2EPUimage acquisition
4cryoSPARCCTF correctionPatchCTF
7Rosettamodel fitting
8PHENIXmodel fitting
10Cootmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335369 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDChain-IDSource nameTypeDetails
11ARoseTTAFoldin silico model
21HLOtherin silico modelhttps://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabpred/abodybuilder2_results/20230713_0236990/
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02124871
ELECTRON MICROSCOPYf_angle_d1.92396597
ELECTRON MICROSCOPYf_chiral_restr0.1069710
ELECTRON MICROSCOPYf_plane_restr0.0098839
ELECTRON MICROSCOPYf_dihedral_angle_d10.42911762

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