Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 438.14 kDa 
• Atom Count: 22895 
• Modelled Residue Count: 2920 
• Deposited Residue Count: 3864 
• Unique protein chains: 1

6XKL

SARS-CoV-2 HexaPro S One RBD up

• PDB DOI: 10.2210/pdb6XKL/pdb
• EM Map EMD-22221:EMDBEMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2020-06-26 Released: 2020-07-15 
• Deposition Author(s): Wrapp, D., Hsieh, C.-L., Goldsmith, J.A., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes.

Hsieh, C.L., Goldsmith, J.A., Schaub, J.M., DiVenere, A.M., Kuo, H.C., Javanmardi, K., Le, K.C., Wrapp, D., Lee, A.G., Liu, Y., Chou, C.W., Byrne, P.O., Hjorth, C.K., Johnson, N.V., Ludes-Meyers, J., Nguyen, A.W., Park, J., Wang, N., Amengor, D., Lavinder, J.J., Ippolito, G.C., Maynard, J.A., Finkelstein, I.J., McLellan, J.S.

(2020) Science 369: 1501-1505

• PubMed: 32703906 
• DOI: 10.1126/science.abd0826
• Primary Citation of Related Structures:  
  6XKL


• PubMed Abstract: 
  

The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

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Related Citations: 

• Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes.
  Hsieh, C.L., Goldsmith, J.A., Schaub, J.M., DiVenere, A.M., Kuo, H.C., Javanmardi, K., Le, K.C., Wrapp, D., Lee, A.G., Liu, Y., Chou, C.W., Byrne, P.O., Hjorth, C.K., Johnson, N.V., Ludes-Meyers, J., Nguyen, A.W., Park, J., Wang, N., Amengor, D., Maynard, J.A., Finkelstein, I.J., McLellan, J.S.
  (2020) Biorxiv --: --

• Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes.
  Hsieh, C.L., Goldsmith, J.A., Schaub, J.M., DiVenere, A.M., Kuo, H.C., Javanmardi, K., Le, K.C., Wrapp, D., Lee, A.G., Liu, Y., Chou, C.W., Byrne, P.O., Hjorth, C.K., Johnson, N.V., Ludes-Meyers, J., Nguyen, A.W., Park, J., Wang, N., Amengor, D., Maynard, J.A., Finkelstein, I.J., McLellan, J.S.
  (2020) Biorxiv --: --

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Organizational Affiliation: 

Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA. [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H, I, J, K, L, M, N	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.21 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-26 
• Released Date: 2020-07-15 
Deposition Author(s): Wrapp, D., Hsieh, C.-L., Goldsmith, J.A., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI127521

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-07-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 3.0: 2020-09-02
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 3.1: 2020-09-30
  Changes: Database references