Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.43 kDa 
• Atom Count: 3238 
• Residue Count: 388 
• Unique protein chains: 2

5JQB

Crystal structure of Ebola glycoprotein in complex with ibuprofen

• DOI: 10.2210/pdb5JQB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Mayinga, Zaire, 1976
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-05-04 Released: 2016-06-29 
• Deposition Author(s): Zhao, Y., Ren, J., Stuart, D.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Toremifene interacts with and destabilizes the Ebola virus glycoprotein.

Zhao, Y., Ren, J., Harlos, K., Jones, D.M., Zeltina, A., Bowden, T.A., Padilla-Parra, S., Fry, E.E., Stuart, D.I.

(2016) Nature 535: 168-172

• PubMed: 27362232 
• DOI: 10.1038/nature18615
• Primary Citation of Related Structures:  
  5JQ7, 5JQ3, 5JQB


• PubMed Abstract: 
  

Ebola viruses (EBOVs) are responsible for repeated outbreaks of fatal infections, including the recent deadly epidemic in West Africa. There are currently no approved therapeutic drugs or vaccines for the disease. EBOV has a membrane envelope decorated by trimers of a glycoprotein (GP, cleaved by furin to form GP1 and GP2 subunits), which is solely responsible for host cell attachment, endosomal entry and membrane fusion. GP is thus a primary target for the development of antiviral drugs. Here we report the first, to our knowledge, unliganded structure of EBOV GP, and high-resolution complexes of GP with the anticancer drug toremifene and the painkiller ibuprofen. The high-resolution apo structure gives a more complete and accurate picture of the molecule, and allows conformational changes introduced by antibody and receptor binding to be deciphered. Unexpectedly, both toremifene and ibuprofen bind in a cavity between the attachment (GP1) and fusion (GP2) subunits at the entrance to a large tunnel that links with equivalent tunnels from the other monomers of the trimer at the three-fold axis. Protein–drug interactions with both GP1 and GP2 are predominately hydrophobic. Residues lining the binding site are highly conserved among filoviruses except Marburg virus (MARV), suggesting that MARV may not bind these drugs. Thermal shift assays show up to a 14 °C decrease in the protein melting temperature after toremifene binding, while ibuprofen has only a marginal effect and is a less potent inhibitor. These results suggest that inhibitor binding destabilizes GP and triggers premature release of GP2, thereby preventing fusion between the viral and endosome membranes. Thus, these complex structures reveal the mechanism of inhibition and may guide the development of more powerful anti-EBOV drugs.

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Organizational Affiliation: 

Diamond Light Source Ltd, Harwell Science &Innovation Campus, Didcot, OX11 0DE, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1	A	330	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 1  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein 2	B	168	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IBP	B	IBUPROFEN C13 H18 O2 HEFNNWSXXWATRW-JTQLQIEISA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.76	α = 90
b = 113.76	β = 90
c = 306.15	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-04 
• Released Date: 2016-06-29 
Deposition Author(s): Zhao, Y., Ren, J., Stuart, D.I.

Revision History 

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary