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- EMDB-11328: SARS-CoV-2 spike in prefusion state -

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Basic information

Entry
Database: EMDB / ID: EMD-11328
TitleSARS-CoV-2 spike in prefusion state
Map data
SampleSpike homotrimer in prefusion state:
Spike glycoprotein / (ligand) x 4
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMartinez M / Marabini R / Carazo JM
Funding support Spain, European Union, United States, 5 items
OrganizationGrant numberCountry
Spanish National Research CouncilPIE/COVID-19 202020E079 Spain
European Research Council (ERC)ERC - 2018 - SyG, Proposal: 810057European Union
Spanish Ministry of Science, Innovation, and UniversitiesSEV 2017-0712 Spain
National Institutes of Health/National Library of Medicine (NIH/NLM)R01-AI127521 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)GM125769 United States
CitationJournal: bioRxiv / Year: 2020
Title: Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.
Abstract: With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We ...With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.
Validation ReportPDB-ID: 6zow

SummaryFull reportAbout validation report
History
DepositionJul 7, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.129
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.129
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zow
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11328.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 432 pix.
= 452.304 Å
1.05 Å/pix.
x 432 pix.
= 452.304 Å
1.05 Å/pix.
x 432 pix.
= 452.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density
Contour LevelBy AUTHOR: 0.129 / Movie #1: 0.129
Minimum - Maximum-0.5702415 - 1.6117468
Average (Standard dev.)-0.00040706724 (±0.028517144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 452.30402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z452.304452.304452.304
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.5701.612-0.000

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Supplemental data

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Additional map: #1

Fileemd_11328_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #2

Fileemd_11328_additional_2.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_11328_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_11328_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire Spike homotrimer in prefusion state

EntireName: Spike homotrimer in prefusion state / Number of components: 6

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Component #1: protein, Spike homotrimer in prefusion state

ProteinName: Spike homotrimer in prefusion state / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Vector: palphaH / Cell of expression system: FreeStyle293F

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 141.263344 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #4: ligand, alpha-D-mannopyranose

LigandName: alpha-D-mannopyranose / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #5: ligand, DIMETHYL SULFOXIDE

LigandName: DIMETHYL SULFOXIDE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 7.813305 MDa

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Component #6: ligand, water

LigandName: water / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 203000
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Details: Initial models 6VSB and 6VYB were used for flexible fitting, whereas 6YLA was used for rigid fitting of the RBD domain of chain A, that we have called a in the final structure.
Input PDB model: 6VSB, 6VSB, 6VSB, 6VSB, 6VYB, 6VYB, 6VYB, 6VYB, 6YLA
Chain ID: A, A, B, C, A, A, B, C, A
Output model

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