4C53

Crystal Structure of Guanarito virus GP2 in the post-fusion conformation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.14 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

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This is version 2.1 of the entry. See complete history. 


Literature

Crystal Structure of Venezuelan Hemorrhagic Fever Virus Fusion Glycoprotein Reveals a Class 1 Post-Fusion Architecture with Extensive Glycosylation.

Parsy, M., Harlos, K., Huiskonen, J.T., Bowden, T.A.

(2013) J Virol 87: 13070

  • DOI: https://doi.org/10.1128/JVI.02298-13
  • Primary Citation of Related Structures:  
    4C53

  • PubMed Abstract: 

    Guanarito virus (GTOV) is an emergent and deadly pathogen. We present the crystal structure of the glycosylated GTOV fusion glycoprotein to 4.1-Å resolution in the postfusion conformation. Our structure reveals a classical six-helix bundle and presents direct verification that New World arenaviruses exhibit class I viral membrane fusion machinery. The structure provides visualization of an N-linked glycocalyx coat, and consideration of glycan dynamics reveals extensive coverage of the underlying protein surface, following virus-host membrane fusion.

    • Organizational Affiliation: 

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
A, B, C
138Mammarenavirus guanaritoenseMutation(s): 0 
UniProt
Find proteins for Q8AYW1 (Guanarito mammarenavirus (isolate Human/Venezuela/NH-95551/1990))
Explore Q8AYW1 
Go to UniProtKB:  Q8AYW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8AYW1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, H
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.14 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.5α = 90
b = 98.5β = 90
c = 78.74γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary