6XKL

SARS-CoV-2 HexaPro S One RBD up


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


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

  • 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 ...

    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).


    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 --: --

    Organizational Affiliation

    Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA. maynard@che.utexas.edu ilya@finkelsteinlab.org jmclellan@austin.utexas.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinABC1288Severe acute respiratory syndrome coronavirus 2Mutation(s): 6 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
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 Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-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