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- PDB-8tqi: Hemagglutinin-neuraminidase from Human parainfluenza virus type 3... -

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Basic information

Entry
Database: PDB / ID: 8tqi
TitleHemagglutinin-neuraminidase from Human parainfluenza virus type 3: complex with rPIV3-23 and rPIV3-28 Fabs
Components
  • Heavy chain Fab rPIV3-23
  • Heavy chain Fab rPIV3-28
  • Hemagglutinin-neuraminidase
  • Light chain Fab rPIV3-23
  • Light chain Fab rPIV3-28
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immune system / viral neutralization / VIRAL PROTEIN / 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 / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin-neuraminidase
Similarity search - Component
Biological speciesHuman respirovirus 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsOtrelo-Cardoso, A.R. / Jardetzky, T.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI13752 United States
CitationJournal: To Be Published
Title: Functional and structural characteristics of human monoclonal antibodies that potently neutralize human parainfluenza virus type 3
Authors: Suryadevara, N. / Otrelo-Cardoso, A.R. / Kose, N. / Hu, Y.X. / Binshtein, E. / Wolters, R. / Drew-Bear, J. / Handal, L.S. / Carnahan, R.H. / Moscona, A. / Jardetzky, T.S. / Crowe Jr, J.E.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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: Hemagglutinin-neuraminidase
B: Hemagglutinin-neuraminidase
C: Heavy chain Fab rPIV3-28
D: Light chain Fab rPIV3-28
E: Heavy chain Fab rPIV3-23
F: Light chain Fab rPIV3-23
H: Heavy chain Fab rPIV3-28
L: Light chain Fab rPIV3-28
I: Heavy chain Fab rPIV3-23
J: Light chain Fab rPIV3-23


Theoretical massNumber of molelcules
Total (without water)291,94710
Polymers291,94710
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hemagglutinin-neuraminidase


Mass: 50774.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respirovirus 3 / Gene: HN / Cell line (production host): HEK / Production host: Homo sapiens (human) / Strain (production host): 293 6e / References: UniProt: P08492
#2: Antibody Heavy chain Fab rPIV3-28


Mass: 23344.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Light chain Fab rPIV3-28


Mass: 23592.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Heavy chain Fab rPIV3-23


Mass: 24952.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody Light chain Fab rPIV3-23


Mass: 23309.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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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

Component
IDNameTypeEntity IDParent-IDSource
1HPIV3 HN in complex with rPIV3-23 and rPIV3-28 FabsCOMPLEXall0MULTIPLE SOURCES
2Hemagglutinin-neuraminidase glycoproteinCOMPLEX#11RECOMBINANT
3Recombinant rPIV3-28 FabCOMPLEX#2-#31RECOMBINANT
4Recombinant rPIV3-23 FabCOMPLEX#4-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
31NO
41NO
51NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human respirovirus 311216
32Human respirovirus 311216
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
21Homo sapiens (human)9606293 6eHEKPTT5
32Homo sapiens (human)9606293 6eHEKPTT5
43Cricetulus griseus (Chinese hamster)10029CHO
54Cricetulus griseus (Chinese hamster)10029CHO
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47827 / Symmetry type: POINT

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