8TQK | pdb_00008tqk

Human parainfluenza virus type 3 prefusion F trimer in complex with rPIV3-18 Fab

• PDB DOI: https://doi.org/10.2210/pdb8TQK/pdb
• EM Map EMD-41506: EMDB EMDataResource

• Classification: VIRAL PROTEIN, IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human respirovirus 3
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-08-07 Released: 2024-04-24 
• Deposition Author(s): Otrelo-Cardoso, A.R., Jardetzky, T.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Functional and structural basis of human parainfluenza virus type 3 neutralization with human monoclonal antibodies.

Suryadevara, N., Otrelo-Cardoso, A.R., Kose, N., Hu, Y.X., Binshtein, E., Wolters, R.M., Greninger, A.L., Handal, L.S., Carnahan, R.H., Moscona, A., Jardetzky, T.S., Crowe Jr., J.E.

(2024) Nat Microbiol 9: 2128-2143

• PubMed: 38858594 
• DOI: https://doi.org/10.1038/s41564-024-01722-w
• Primary Citation Related Structures: 
  8TQI, 8TQK


• PubMed 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 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.

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Organizational Affiliation: 
• Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA.
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
Departments of Pediatrics, Microbiology and Immunology, and Physiology and Cellular Biophysics, and Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].
Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].
Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 314.97 kDa 
• Atom Count: 14,725 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 2,862 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain Fab rPIV3-18	A [auth D], C [auth F], E [auth H]	224	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain Fab rPIV3-28	B [auth E], D [auth G], F [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	G [auth A], H [auth B], I [auth C]	516	Human respirovirus 3	Mutation(s): 6  Gene Names: F, KMQ_34898gpF
UniProt
Find proteins for A0A059QA82 (Human respirovirus 3) Explore A0A059QA82  Go to UniProtKB:  A0A059QA82

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Otrelo-Cardoso, A.R., Jardetzky, T.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI13752

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references
• Version 1.3: 2025-05-14
  Changes: Data collection