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- EMDB-13919: SARS-CoV-2 S protein S:D614G mutant 1-up -

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Basic information

Entry
Database: EMDB / ID: EMD-13919
TitleSARS-CoV-2 S protein S:D614G mutant 1-up
Map dataSARS-CoV-2 S protein S:D614G mutant 1-up
Sample
  • Complex: SARS-CoV-2 S protein S:D614G mutant
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome-related coronavirus / Escherichia virus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGinex T / Marco-Marin C / Wieczor M / Mata CP / Krieger J / Lopez-Redondo ML / Frances-Gomez C / Ruiz-Rodriguez P / Melero R / Sanchez-Sorzano CO ...Ginex T / Marco-Marin C / Wieczor M / Mata CP / Krieger J / Lopez-Redondo ML / Frances-Gomez C / 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-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13919.png

Downloads & links

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Map

FileDownload / File: emd_13919.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 S protein S:D614G mutant 1-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: 0.057
Minimum - Maximum-0.0016482698 - 1.5133927
Average (Standard dev.)0.00095763133 (±0.019435013)
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:D614G mutant 1-up unsharpened map

Fileemd_13919_additional_1.map
AnnotationSARS-CoV-2 S protein S:D614G mutant 1-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:D614G mutant 1-up half map 1

Fileemd_13919_half_map_1.map
AnnotationSARS-CoV-2 S protein S:D614G mutant 1-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:D614G mutant 1-up half map 2

Fileemd_13919_half_map_2.map
AnnotationSARS-CoV-2 S protein S:D614G mutant 1-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:D614G mutant

EntireName: SARS-CoV-2 S protein S:D614G mutant
Components
  • Complex: SARS-CoV-2 S protein S:D614G mutant
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: SARS-CoV-2 S protein S:D614G mutant / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia virus T4
Molecular weightTheoretical: 138.902688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLGV YYHKNNKSWM ESEFRVYSSA NNCTFEYVSQ P FLMDLEGK ...String:
CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGTN GTKRFDNPVL PFNDGVYFAS TEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLGV YYHKNNKSWM ESEFRVYSSA NNCTFEYVSQ P FLMDLEGK QGNFKNLREF VFKNIDGYFK IYSKHTPINL VRDLPQGFSA LEPLVDLPIG INITRFQTLL ALHRSYLTPG DS SSGWTAG AAAYYVGYLQ PRTFLLKYNE NGTITDAVDC ALDPLSETKC TLKSFTVEKG IYQTSNFRVQ PTESIVRFPN ITN LCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQ TGKIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVEGFNCY FPLQS YGFQ PTNGVGYQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTESNKK FLPFQQFGRD IADTTD AVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVPVAIHAD QLTPTWRVYS TGSNVFQTRA GCLIGAE HV NNSYECDIPI GAGICASYQT QTNSPASVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVD C TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKDFG GFNFSQILPD PSKPSKRSF IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGAALQIP FAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTASALG KLQDVVNQNA QALNTLVKQL SSNFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS AP HGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTV YDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESLIDLQEL GKYEQYIKWP LVPR GSGYI PEAPRDGQAY VRKDGEWVFL STFLSPHHHH HHHHHEQKLI SEEDL

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
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: 2492 / 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: 268763
CTF correctionSoftware: (Name: CTFFIND, Gctf, cryoSPARC)
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82102

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

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

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