8EAY | pdb_00008eay

HMPV F complex with 4I3 Fab

• PDB DOI: https://doi.org/10.2210/pdb8EAY/pdb
• EM Map EMD-27990: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Human metapneumovirus A, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-08-30 Released: 2023-08-16 
• Deposition Author(s): Wen, X., 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: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Potent cross-neutralization of respiratory syncytial virus and human metapneumovirus through a structurally conserved antibody recognition mode.

Wen, X., Suryadevara, N., Kose, N., Liu, J., Zhan, X., Handal, L.S., Williamson, L.E., Trivette, A., Carnahan, R.H., Jardetzky, T.S., Crowe Jr., J.E.

(2023) Cell Host Microbe 31: 1288-1300.e6

• PubMed: 37516111 
• DOI: https://doi.org/10.1016/j.chom.2023.07.002
• Primary Citation Related Structures: 
  8DZW, 8E2U, 8EAY, 8EBP


• PubMed Abstract: 
  

  Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F antibodies from a human donor. One antibody (RSV-199) potently cross-neutralized 8 RSV and hMPV strains by recognizing antigenic site III, which is partially conserved in RSV and hMPV F. Next, we determined the cryoelectron microscopy (cryo-EM) structures of RSV-199 bound to RSV F trimers, hMPV F monomers, and an unexpected dimeric form of hMPV F. These structures revealed how RSV-199 engages both RSV and hMPV F proteins through conserved interactions of the antibody heavy-chain variable region and how variability within heavy-chain complementarity-determining region 3 (HCDR3) can be accommodated at the F protein interface in site-III-directed antibodies. Furthermore, RSV-199 offered enhanced protection against RSV A and B strains and hMPV in cotton rats. These findings highlight the mechanisms of broad neutralization and therapeutic potential of RSV-199.

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Organizational Affiliation: 
• Department of Structural Biology, Stanford University School of Medical School, Stanford, CA 94305, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
Department of Structural Biology, Stanford University School of Medical School, Stanford, CA 94305, USA. Electronic address: [e-mail].
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.86 kDa 
• Atom Count: 4,761 
• Modeled Residue Count: 626 
• Deposited Residue Count: 642 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A	414	Human metapneumovirus A	Mutation(s): 0
UniProt
Find proteins for Q8B9P0 (human metapneumovirus) Explore Q8B9P0  Go to UniProtKB:  Q8B9P0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4I3 heavy chain protein	B [auth H]	121	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
4I3 light chain protein	C [auth L]	107	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Wen, X., 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	R01AI137523

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release
  
• Version 1.1: 2023-08-23
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary