4DAG

Structure of the Human Metapneumovirus Fusion Protein with Neutralizing Antibody Identifies a Pneumovirus Antigenic Site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Structure of the human metapneumovirus fusion protein with neutralizing antibody identifies a pneumovirus antigenic site.

Wen, X., Krause, J.C., Leser, G.P., Cox, R.G., Lamb, R.A., Williams, J.V., Crowe, J.E., Jardetzky, T.S.

(2012) Nat Struct Mol Biol 19: 461-463

  • DOI: https://doi.org/10.1038/nsmb.2250
  • Primary Citation of Related Structures:  
    4DAG

  • PubMed Abstract: 

    Human metapneumovirus and respiratory syncytial virus cause lower respiratory tract infections. The virus fusion (F) glycoprotein promotes membrane fusion by refolding from a metastable pre-fusion to a stable post-fusion conformation. F is also a major target of the neutralizing antibody response. Here we show that a potently neutralizing anti-human metapneumovirus antibody (DS7) binds a structurally invariant domain of F, revealing a new epitope that could be targeted in vaccine development.

    • Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0415human metapneumovirusMutation(s): 0 
UniProt
Find proteins for G3KCK8 (human metapneumovirus)
Explore G3KCK8 
Go to UniProtKB:  G3KCK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3KCK8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neutralizing Antibody DS7 heavy chainB [auth H]220Homo sapiensMutation(s): 0 
Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
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UniProt GroupP01857
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Neutralizing Antibody DS7 light chainC [auth L]213Homo sapiensMutation(s): 0 
Gene Names: IGL@
UniProt
Find proteins for Q8N5F4 (Homo sapiens)
Explore Q8N5F4 
Go to UniProtKB:  Q8N5F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N5F4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B],
E [auth C]		5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258.96α = 90
b = 258.96β = 90
c = 167.36γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-04-04
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary