Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 30.13 kDa 
• Atom Count: 1997 
• Modelled Residue Count: 240 
• Deposited Residue Count: 254 
• Unique protein chains: 1

6H3V

Bunyamwera Virus Glycoprotein Gc Head Domain

• PDB DOI: 10.2210/pdb6H3V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bunyamwera virus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-07-19 Released: 2019-02-27 
• Deposition Author(s): Hellert, J., Aebischer, A., Wernike, K., Haouz, A., Brocchi, E., Reiche, S., Guardado-Calvo, P., Beer, M., Rey, F.A.
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.167 
• R-Value Observed: 0.172 

Literature

Orthobunyavirus spike architecture and recognition by neutralizing antibodies.

Hellert, J., Aebischer, A., Wernike, K., Haouz, A., Brocchi, E., Reiche, S., Guardado-Calvo, P., Beer, M., Rey, F.A.

(2019) Nat Commun 10: 879-879

• PubMed: 30787296 
• DOI: 10.1038/s41467-019-08832-8
• Primary Citation of Related Structures:  
  6H3S, 6H3T, 6H3U, 6H3V, 6H3W, 6H3X


• PubMed Abstract: 
  

Orthobunyaviruses (OBVs) form a distinct genus of arthropod-borne bunyaviruses that can cause severe disease upon zoonotic transmission to humans. Antigenic drift or genome segment re-assortment have in the past resulted in new pathogenic OBVs, making them potential candidates for causing emerging zoonoses in the future. Low-resolution electron cryo-tomography studies have shown that OBV particles feature prominent trimeric spikes, but their molecular organization remained unknown. Here we report X-ray crystallography studies of four different OBVs showing that the spikes are formed by an N-terminal extension of the fusion glycoprotein Gc. Using Schmallenberg virus, a recently emerged OBV, we also show that the projecting spike is the major target of the neutralizing antibody response, and provide X-ray structures in complex with two protecting antibodies. We further show that immunization of mice with the spike domains elicits virtually sterilizing immunity, providing fundamental knowledge essential in the preparation for potential newly emerging OBV zoonoses.

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Organizational Affiliation: 

Structural Virology Unit, Virology Department, Institut Pasteur, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015, Paris, France. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	A	254	Bunyamwera virus	Mutation(s): 0  Gene Names: GP
UniProt
Find proteins for P04505 (Bunyamwera virus) Explore P04505  Go to UniProtKB:  P04505

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.167 
• R-Value Observed: 0.172 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.44	α = 90
b = 125.44	β = 90
c = 46.55	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-19 
• Released Date: 2019-02-27 
Deposition Author(s): Hellert, J., Aebischer, A., Wernike, K., Haouz, A., Brocchi, E., Reiche, S., Guardado-Calvo, P., Beer, M., Rey, F.A.

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative		115760

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary