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Open data
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Basic information
Entry | Database: PDB / ID: 7qdg | |||||||||||||||||||||||||||
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Title | SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up | |||||||||||||||||||||||||||
![]() | Spike glycoprotein,Fibritin | |||||||||||||||||||||||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / S protein / S:A222V + S:D614G mutant | |||||||||||||||||||||||||||
Function / homology | ![]() 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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / 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 / 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 | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||||||||
![]() | 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. ...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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 654.9 KB | Display | ![]() |
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PDB format | ![]() | 526.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 121.2 KB | Display | |
Data in CIF | ![]() | 163.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13916MC ![]() 7qdhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 138930.734 Da / Num. of mol.: 3 / Mutation: S:A222V + S:D614G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2, wac / Variant: 20E (EU1) / Production host: ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: SARS-CoV-2 S protein S:A222V + S:D614G mutant / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.34 MDa / Experimental value: NO | |||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||
Details of virus | Empty: YES | |||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 120000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 300 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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: 4841 |
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Processing
Software | Name: REFMAC / Version: 5.8.0158 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 509466 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145681 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7BNN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.4→420 Å / Cor.coef. Fo:Fc: 0.598 / SU B: 7.797 / SU ML: 0.125 / ESU R: 0.113 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.136 Å2
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Refinement step | Cycle: 1 / Total: 25557 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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