1WYY | pdb_00001wyy

Post-fusion hairpin conformation of the sars coronavirus spike glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb1WYY/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-02-18 Released: 2005-05-17 
• Deposition Author(s): Duquerroy, S., Vigouroux, A., Rottier, P.J.M., Rey, F.A., Bosch, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.249 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein

Duquerroy, S., Vigouroux, A., Rottier, P.J.M., Rey, F.A., Bosch, B.J.

(2005) Virology 335: 276-285

• PubMed: 15840526 
• DOI: https://doi.org/10.1016/j.virol.2005.02.022
• Primary Citation Related Structures: 
  1WYY


• PubMed Abstract: 
  

  The coronavirus spike glycoprotein is a class I membrane fusion protein with two characteristic heptad repeat regions (HR1 and HR2) in its ectodomain. Here, we report the X-ray structure of a previously characterized HR1/HR2 complex of the severe acute respiratory syndrome coronavirus spike protein. As expected, the HR1 and HR2 segments are organized in antiparallel orientations within a rod-like molecule. The HR1 helices form an exceptionally long (120 A) internal coiled coil stabilized by hydrophobic and polar interactions. A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding "zippers" that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 alpha-helix.

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Organizational Affiliation: 
• Laboratoire de Virologie Moléculaire and Structurale, UMR 2472/1157 CNRS-INRA and IFR 115, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 32.47 kDa 
• Atom Count: 2,030 
• Modeled Residue Count: 250 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 Glycoprotein	A, B	149	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: S
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594  Go to UniProtKB:  P59594

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.249 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.983	α = 90
b = 41.983	β = 90
c = 320.544	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-17 
Deposition Author(s): Duquerroy, S., Vigouroux, A., Rottier, P.J.M., Rey, F.A., Bosch, B.J.

Revision History  

• Version 1.0: 2005-05-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-04-23
  Changes: Experimental preparation
• Version 1.4: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description