7M0I | pdb_00007m0i

Crystal structure of a human metapneumovirus subtype B2 trimeric fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.291 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure, Immunogenicity, and Conformation-Dependent Receptor Binding of the Postfusion Human Metapneumovirus F Protein.

Huang, J.Chopra, P.Liu, L.Nagy, T.Murray, J.Tripp, R.A.Boons, G.J.Mousa, J.J.

(2021) J Virol 95: e0059321-e0059321

  • DOI: https://doi.org/10.1128/JVI.00593-21
  • Primary Citation Related Structures: 
    7M0I

  • PubMed Abstract: 

    Human metapneumovirus (hMPV) is an important cause of acute viral respiratory infection. As the only target of neutralizing antibodies, the hMPV fusion (F) protein has been a major focus for vaccine development and targeting by drugs and monoclonal antibodies (MAbs). While X-ray structures of trimeric prefusion and postfusion hMPV F proteins from genotype A, and monomeric prefusion hMPV F protein from genotype B have been determined, structural data for the postfusion conformation for genotype B is lacking. We determined the crystal structure of this protein and compared the structural differences of postfusion hMPV F between hMPV A and B genotypes. We also assessed the receptor binding properties of the hMPV F protein to heparin and heparan sulfate (HS). A library of HS oligomers was used to verify the HS binding activity of hMPV F, and several compounds showed binding to predominantly prefusion hMPV F, but had limited binding to postfusion hMPV F. Furthermore, MAbs to antigenic sites III and the 66-87 intratrimeric epitope block heparin binding. In addition, we evaluated the efficacy of postfusion hMPV B2 F protein as a vaccine candidate in BALB/c mice. Mice immunized with hMPV B2 postfusion F protein showed a balanced Th1/Th2 immune response and generated neutralizing antibodies against both subgroup A2 and B2 hMPV strains, which protected the mice from hMPV challenge. Antibody competition analysis revealed the antibodies generated by immunization target two known antigenic sites (III and IV) on the hMPV F protein. Overall, this study provides new characteristics of the hMPV F protein, which may be informative for vaccine and therapy development. IMPORTANCE Human metapneumovirus (hMPV) is an important cause of viral respiratory disease. In this paper, we report the X-ray crystal structure of the hMPV fusion (F) protein in the postfusion conformation from genotype B. We also assessed binding of the hMPV F protein to heparin and heparan sulfate, a previously reported receptor for the hMPV F protein. Furthermore, we determined the immunogenicity and protective efficacy of postfusion hMPV B2 F protein, which is the first study using a homogenous conformation of the protein. Antibodies generated in response to vaccination give a balanced Th1/Th2 response and target two previously discovered neutralizing epitopes.


  • Organizational Affiliation
    • Department of Infectious Diseases, College of Veterinary Medicine, University of Georgiagrid.213876.9, Athens, Georgia, USA.

Macromolecule Content 

  • Total Structure Weight: 346.04 kDa 
  • Atom Count: 19,556 
  • Modeled Residue Count: 2,530 
  • Deposited Residue Count: 3,120 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion glycoprotein F289human metapneumovirusMutation(s): 0 
UniProt
Find proteins for C6F474 (human metapneumovirus)
Explore C6F474 
Go to UniProtKB:  C6F474
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6F474
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion glycoprotein F1431human metapneumovirusMutation(s): 0 
UniProt
Find proteins for C6F474 (human metapneumovirus)
Explore C6F474 
Go to UniProtKB:  C6F474
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6F474
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth E]
CA [auth F]
DA [auth F]
M [auth G]
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth F],
M [auth G],
N [auth H],
O [auth H],
P [auth I],
Q [auth J],
R [auth J],
S [auth K],
T [auth L],
U [auth L],
V [auth A],
W [auth B],
X [auth B],
Y [auth C],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.291 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.53α = 90
b = 128.1β = 90
c = 431.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI14386

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary