7KRR

Structural impact on SARS-CoV-2 spike protein by D614G substitution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural impact on SARS-CoV-2 spike protein by D614G substitution.

Zhang, J.Cai, Y.Xiao, T.Lu, J.Peng, H.Sterling, S.M.Walsh Jr., R.M.Rits-Volloch, S.Zhu, H.Woosley, A.N.Yang, W.Sliz, P.Chen, B.

(2021) Science 372: 525-530

  • DOI: https://doi.org/10.1126/science.abf2303
  • Primary Citation of Related Structures:  
    7KRQ, 7KRR, 7KRS

  • PubMed Abstract: 

    Substitution for aspartic acid (D) by glycine (G) at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. Here, we report cryo-electron microscopy structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations that differ primarily by the position of one receptor-binding domain. A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer-effectively increasing the number of functional spikes and enhancing infectivity-and to modulate structural rearrangements for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.


  • Organizational Affiliation

    Division of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
B [auth C],
C [auth A]
1,310Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
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
Glycosylation
Glycosylation Sites: 18Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseDA [auth d],
K,
V
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth e],
FA [auth f],
L,
M,
W,
EA [auth e],
FA [auth f],
L,
M,
W,
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth A]
EB [auth A]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GA [auth B],
GB [auth A],
HA [auth B],
HB [auth A],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
OA [auth B],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth A],
YA [auth A],
ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

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 StatesAI147884
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141002

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2021-05-12
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary