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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-sialidase / exo-alpha-sialidase activity / host cell surface receptor binding / viral envelope / symbiont entry into host cell / 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: Nat Microbiol / Year: 2024
Title: Functional and structural basis of human parainfluenza virus type 3 neutralization with human monoclonal antibodies.
Authors: Naveenchandra Suryadevara / Ana Rita Otrelo-Cardoso / Nurgun Kose / Yao-Xiong Hu / Elad Binshtein / Rachael M Wolters / Alexander L Greninger / Laura S Handal / Robert H Carnahan / Anne ...Authors: Naveenchandra Suryadevara / Ana Rita Otrelo-Cardoso / Nurgun Kose / Yao-Xiong Hu / Elad Binshtein / Rachael M Wolters / Alexander L Greninger / Laura S Handal / Robert H Carnahan / Anne Moscona / Theodore S Jardetzky / James E Crowe /
Abstract: Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have ...Human parainfluenza virus type 3 (hPIV3) is a respiratory pathogen that can cause severe disease in older people and infants. Currently, vaccines against hPIV3 are in clinical trials but none have been approved yet. The haemagglutinin-neuraminidase (HN) and fusion (F) surface glycoproteins of hPIV3 are major antigenic determinants. Here we describe naturally occurring potently neutralizing human antibodies directed against both surface glycoproteins of hPIV3. We isolated seven neutralizing HN-reactive antibodies and a pre-fusion conformation F-reactive antibody from human memory B cells. One HN-binding monoclonal antibody (mAb), designated PIV3-23, exhibited functional attributes including haemagglutination and neuraminidase inhibition. We also delineated the structural basis of neutralization for two HN and one F mAbs. MAbs that neutralized hPIV3 in vitro protected against infection and disease in vivo in a cotton rat model of hPIV3 infection, suggesting correlates of protection for hPIV3 and the potential clinical utility of these mAbs.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
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Revision 1.0Apr 24, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 24, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 24, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 24, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 24, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
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Revision 1.2Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.3May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)
Has protein modificationY

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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
8PHENIXmodel refinement
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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