7JJI

Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.

Bangaru, S.Ozorowski, G.Turner, H.L.Antanasijevic, A.Huang, D.Wang, X.Torres, J.L.Diedrich, J.K.Tian, J.H.Portnoff, A.D.Patel, N.Massare, M.J.Yates 3rd, J.R.Nemazee, D.Paulson, J.C.Glenn, G.Smith, G.Ward, A.B.

(2020) Science 370: 1089-1094

  • DOI: 10.1126/science.abe1502
  • Primary Citation of Related Structures:  
    7JJI, 7JJJ

  • PubMed Abstract: 
  • Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies ...

    Vaccine efforts to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the current coronavirus disease 2019 (COVID-19) pandemic, are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. We also observed interactions between the spike trimers, allowing formation of higher-order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.


    Related Citations: 
    • Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.
      Bangaru, S., Ozorowski, G., Turner, H.L., Antanasijevic, A., Huang, D., Wang, X., Torres, J.L., Diedrich, J.K., Tian, J.H., Portnoff, A.D., Patel, N., Massare, M.J., Yates, J.R., Nemazee, D., Paulson, J.C., Glenn, G., Smith, G., Ward, A.B.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. andrew@scripps.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA, B, C1273Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
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
AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, EA [auth e], F
AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, X, Y, Z
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VCG
Query on VCG

Download Ideal Coordinates CCD File 
BB [auth B], EB [auth C], XA [auth A]2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside
C32 H60 O10
RGPBUVUVZKQNHD-YPJAPDKZSA-N
 Ligand Interaction
EIC
Query on EIC

Download Ideal Coordinates CCD File 
CB [auth C], YA [auth A], ZA [auth B]LINOLEIC ACID
C18 H32 O2
OYHQOLUKZRVURQ-HZJYTTRNSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B], DB [auth C], WA [auth A]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: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references