7QDH

SARS-CoV-2 S protein S:D614G mutant 1-up


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

Ginex, T.Marco-Marin, C.Wieczor, M.Mata, C.P.Krieger, J.Ruiz-Rodriguez, P.Lopez-Redondo, M.L.Frances-Gomez, C.Melero, R.Sanchez-Sorzano, C.O.Martinez, M.Gougeard, N.Forcada-Nadal, A.Zamora-Caballero, S.Gozalbo-Rovira, R.Sanz-Frasquet, C.Arranz, R.Bravo, J.Rubio, V.Marina, A.Geller, R.Comas, I.Gil, C.Coscolla, M.Orozco, M.Llacer, J.L.Carazo, J.M.

(2022) PLoS Pathog 18: e1010631-e1010631

  • DOI: https://doi.org/10.1371/journal.ppat.1010631
  • Primary Citation of Related Structures:  
    7QDG, 7QDH

  • PubMed Abstract: 

    The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,Fibritin
A, B, C
1,250Severe acute respiratory syndrome coronavirus 2Tequatrovirus T4
This entity is chimeric
Mutation(s): 0 
Gene Names: S2wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2P10104
Sequence Annotations
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  • 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 [auth E],
E [auth G],
F [auth I],
G [auth J],
H [auth K],
D [auth E],
E [auth G],
F [auth I],
G [auth J],
H [auth K],
I [auth L],
J [auth M],
K [auth N],
L [auth O],
M [auth P]
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 C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
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: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-104757RB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-094399-A-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainGrant SEV 2017-0712
H2020 Marie Curie Actions of the European CommissionSpainMSCA IF 2020, Proposal: 101024130
European Research Council (ERC)SpainHighResCells, ERC - 2018 - SyG, Proposal: 810057
Spanish National Research CouncilSpainCSIC PTI Salud Global Proposal: 202080E110
European Research Council (ERC)SpainERC CoG 101001038
Spanish Ministry of Science, Innovation, and UniversitiesSpainSEJI/2019/011

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references