6XS6

SARS-CoV-2 Spike D614G variant, minus RBD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.

Yurkovetskiy, L.Wang, X.Pascal, K.E.Tomkins-Tinch, C.Nyalile, T.P.Wang, Y.Baum, A.Diehl, W.E.Dauphin, A.Carbone, C.Veinotte, K.Egri, S.B.Schaffner, S.F.Lemieux, J.E.Munro, J.B.Rafique, A.Barve, A.Sabeti, P.C.Kyratsous, C.A.Dudkina, N.V.Shen, K.Luban, J.

(2020) Cell 183: 739-751.e8

  • DOI: 10.1016/j.cell.2020.09.032
  • Primary Citation of Related Structures:  
    6XS6

  • PubMed Abstract: 
  • The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells ...

    The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.


    Related Citations: 
    • Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
      Yurkovetskiy, L., Wang, X., Pascal, K.E., Tompkins-Tinch, C., Nyalile, T., Wang, Y., Baum, A., Diehl, W.E., Dauphin, A., Carbone, C., Veinotte, K., Egri, S.B., Schaffner, S.F., Lemieux, J.E., Munro, J., Rafique, A., Barve, A., Sabeti, P.C., Kyratsous, C., Dudkina, N., Shen, K., Luban, J.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA. Electronic address: jeremy.luban@umassmed.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinABC1256Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 StatesR37AI147868
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI148784
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesK22CA241362

Revision History 

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references