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- EMDB-13917: SARS-CoV-2 S protein S:A222V + S:D614G mutant 2-up -

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Basic information

Entry
Database: EMDB / ID: EMD-13917
TitleSARS-CoV-2 S protein S:A222V + S:D614G mutant 2-up
Map dataSARS-CoV-2 S protein S:A222V S:D614G mutant 2-up
Sample
  • Complex: SARS-CoV-2 S protein S:A222V + S:D614G mutant
    • Protein or peptide: SARS-CoV-2 S protein S:A222V + S:D614G mutant
KeywordsSARS-CoV-2 / S protein / S:A222V + S:D614G mutant / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsGinex T / Marco-Marin C / Wieczor M / Mata CP / Krieger J / Lopez-Redondo ML / Ruiz-Rodriguez P / Melero R / Sanchez-Sorzano CO / Martinez M ...Ginex T / Marco-Marin C / Wieczor M / Mata CP / Krieger J / Lopez-Redondo ML / Ruiz-Rodriguez P / Melero R / Sanchez-Sorzano CO / 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 JL / Carazo JM
Funding support Spain, 8 items
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, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13917.png

Downloads & links

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Map

FileDownload / File: emd_13917.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 S protein S:A222V S:D614G mutant 2-up
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.0016897683 - 1.8474941
Average (Standard dev.)0.0013904582 (±0.025450755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: SARS-CoV-2 S protein S:A222V S:D614G mutant 2-up unsharpened map

Fileemd_13917_additional_1.map
AnnotationSARS-CoV-2 S protein S:A222V S:D614G mutant 2-up unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV-2 S protein S:A222V S:D614G mutant 2-up half map 1

Fileemd_13917_half_map_1.map
AnnotationSARS-CoV-2 S protein S:A222V S:D614G mutant 2-up half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV-2 S protein S:A222V S:D614G mutant 2-up half map 2

Fileemd_13917_half_map_2.map
AnnotationSARS-CoV-2 S protein S:A222V S:D614G mutant 2-up half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 S protein S:A222V + S:D614G mutant

EntireName: SARS-CoV-2 S protein S:A222V + S:D614G mutant
Components
  • Complex: SARS-CoV-2 S protein S:A222V + S:D614G mutant
    • Protein or peptide: SARS-CoV-2 S protein S:A222V + S:D614G mutant

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Supramolecule #1: SARS-CoV-2 S protein S:A222V + S:D614G mutant

SupramoleculeName: SARS-CoV-2 S protein S:A222V + S:D614G mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: SARS-CoV-2 S protein S:A222V + S:D614G mutant

MacromoleculeName: SARS-CoV-2 S protein S:A222V + S:D614G mutant / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG ...String:
CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP FLMDLEGKQG NFKNLREFVF KNIDGYFKIY SKHTPINLVR DLPQGFSVLE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SSGWTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNITN LCPFGEVFNA TRFASVYAWN RKRISNCVAD YSVLYNSASF STFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGKIADYNYK LPDDFTGCVI AWNSNNLDSK VGGNYNYLYR LFRKSNLKPF ERDISTEIYQ AGSTPCNGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFLPFQQ FGRDIADTTD AVRDPQTLEI LDITPCSFGG VSVITPGTNT SNQVAVLYQG VNCTEVPVAI HADQLTPTWR VYSTGSNVFQ TRAGCLIGAE HVNNSYECDI PIGAGICASY QTQTNSPASV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGDST ECSNLLLQYG SFCTQLNRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQILP DPSKPSKRSF IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVIGIVNNTV YDPLQPELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QYIKWPLVPR GSGYIPEAPR DGQAYVRKDG EWVFLSTFLS PHHHHHHHHH EQKLISEEDL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
10.0 mMHepesHepes pH7.2
150.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4841 / Average exposure time: 20.0 sec. / Average electron dose: 32.4 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 509466
Startup modelType of model: OTHER / Details: Initial model generation
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware: (Name: RELION, Scipion)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4808

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