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: https://doi.org/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).


  • Organizational Affiliation

    Department of Molecular Biosciences, University of Texas, Austin, TX 78712, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 6 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains 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
D, E, F, G, H, I, J, K, L, M, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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  (Full details and data files)

  • 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