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- PDB-7qdh: SARS-CoV-2 S protein S:D614G mutant 1-up -

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Basic information

Entry
Database: PDB / ID: 7qdh
TitleSARS-CoV-2 S protein S:D614G mutant 1-up
ComponentsSpike glycoprotein,Fibritin
KeywordsVIRAL PROTEIN / SARS-CoV-2 / S protein / S:D614G mutant
Function / homology
Function and homology information


virion component / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Escherichia virus T4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGinex, T. / Marco-Marin, C. / Wieczor, M. / Mata, C.P. / Krieger, J. / Lopez-Redondo, M.L. / Frances-Gomez, C. / Ruiz-Rodriguez, P. / Melero, R. / Sanchez-Sorzano, C.O. ...Ginex, T. / Marco-Marin, C. / Wieczor, M. / Mata, C.P. / Krieger, J. / Lopez-Redondo, M.L. / Frances-Gomez, C. / Ruiz-Rodriguez, P. / Melero, R. / Sanchez-Sorzano, C.O. / Martinez, M. / Gougeard, N. / Forcada-Nadal, A. / Zamora-Caballero, S. / Gozalbo-Rovira, R. / Sanz-Frasquet, C. / Bravo, J. / Rubio, V. / Marina, A. / Geller, R. / Comas, I. / Gil, C. / Coscolla, M. / Orozco, M. / LLacer, J.L. / Carazo, J.M.
Funding support Spain, 8items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-104757RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-094399-A-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesGrant SEV 2017-0712 Spain
H2020 Marie Curie Actions of the European CommissionMSCA IF 2020, Proposal: 101024130 Spain
European Research Council (ERC)HighResCells, ERC - 2018 - SyG, Proposal: 810057 Spain
Spanish National Research CouncilCSIC PTI Salud Global Proposal: 202080E110 Spain
European Research Council (ERC)ERC CoG 101001038 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEJI/2019/011 Spain
CitationJournal: PLoS Pathog / Year: 2022
Title: The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.
Authors: Tiziana Ginex / Clara Marco-Marín / Miłosz Wieczór / Carlos P Mata / James Krieger / Paula Ruiz-Rodriguez / Maria Luisa López-Redondo / Clara Francés-Gómez / Roberto Melero / Carlos ...Authors: Tiziana Ginex / Clara Marco-Marín / Miłosz Wieczór / Carlos P Mata / James Krieger / Paula Ruiz-Rodriguez / Maria Luisa López-Redondo / Clara Francés-Gómez / Roberto Melero / Carlos Óscar Sánchez-Sorzano / Marta Martínez / Nadine Gougeard / Alicia Forcada-Nadal / Sara Zamora-Caballero / Roberto Gozalbo-Rovira / Carla Sanz-Frasquet / Rocío Arranz / Jeronimo Bravo / Vicente Rubio / Alberto Marina / / Ron Geller / Iñaki Comas / Carmen Gil / Mireia Coscolla / Modesto Orozco / José Luis Llácer / Jose-Maria Carazo /
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 ...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.
History
DepositionNov 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein,Fibritin
B: Spike glycoprotein,Fibritin
C: Spike glycoprotein,Fibritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)426,26137
Polymers416,7083
Non-polymers9,55334
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Spike glycoprotein,Fibritin / S glycoprotein / E2 / Peplomer protein / Collar protein / Whisker antigen control protein


Mass: 138902.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Escherichia virus T4
Gene: S, 2, wac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2, UniProt: P10104
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SARS-CoV-2 S protein S:D614G mutant / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.34 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome-related coronavirus694009
31Escherichia virus T410665
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepes pH7.2Hepes1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 120000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 300 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 20 sec. / Electron dose: 32.4 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2492

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameCategory
2crYOLOparticle selection
3Scipionparticle selection
4EPUimage acquisition
6CTFFINDCTF correction
7GctfCTF correction
8cryoSPARCCTF correction
11UCSF Chimeramodel fitting
12Cootmodel fitting
14cryoSPARCinitial Euler assignment
15cryoSPARCfinal Euler assignment
16RELIONclassification
17Scipionclassification
18cryoSPARC3D reconstruction
19REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 268763
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82102 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
RefinementResolution: 4.2→420 Å / Cor.coef. Fo:Fc: 0.542 / SU B: 42.445 / SU ML: 0.547 / ESU R: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.55593 --
obs0.55593 2093892 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 196.469 Å2
Baniso -1Baniso -2Baniso -3
1--7 Å2-3.31 Å20.12 Å2
2--1.98 Å2-0.6 Å2
3---5.01 Å2
Refinement stepCycle: 1 / Total: 25703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.0226367
ELECTRON MICROSCOPYr_bond_other_d0.0050.0223445
ELECTRON MICROSCOPYr_angle_refined_deg1.5581.97235988
ELECTRON MICROSCOPYr_angle_other_deg1.396354586
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.04653203
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.3124.6951180
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.598154041
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.39415104
ELECTRON MICROSCOPYr_chiral_restr0.0850.24150
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.02129196
ELECTRON MICROSCOPYr_gen_planes_other0.0050.025360
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.29720.07412850
ELECTRON MICROSCOPYr_mcbond_other3.29720.07412850
ELECTRON MICROSCOPYr_mcangle_it6.1830.10516032
ELECTRON MICROSCOPYr_mcangle_other6.1830.10616033
ELECTRON MICROSCOPYr_scbond_it1.59620.84313517
ELECTRON MICROSCOPYr_scbond_other1.59520.84413518
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.49231.17119957
ELECTRON MICROSCOPYr_long_range_B_refined22.04105597
ELECTRON MICROSCOPYr_long_range_B_other22.04105598
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.2→4.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.561 154585 -
Rfree-0 -
obs--100 %

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