7SEM | pdb_00007sem

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins.

Hsieh, C.L.Rush, S.A.Palomo, C.Chou, C.W.Pickens, W.Mas, V.McLellan, J.S.

(2022) Nat Commun 13: 1299-1299

  • DOI: https://doi.org/10.1038/s41467-022-28931-3
  • Primary Citation Related Structures: 
    7SEJ, 7SEM

  • PubMed Abstract: 

    The human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15 mg/L and has a melting temperature of 71.9 °C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.


  • Organizational Affiliation
    • Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 107.78 kDa 
  • Atom Count: 6,595 
  • Modeled Residue Count: 848 
  • Deposited Residue Count: 995 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MPE8 Fab heavy chainA [auth B]228Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0B [auth F]551human metapneumovirusMutation(s): 0 
UniProt
Find proteins for H6X1Z0 (human metapneumovirus)
Explore H6X1Z0 
Go to UniProtKB:  H6X1Z0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6X1Z0
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MPE8 Fab light chain216Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.169α = 90
b = 45.56β = 94.21
c = 176.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Robert A. Welch FoundationUnited StatesF-0003-19620604
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary