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- EMDB-11347: Structure of SARS-CoV-2 spike glycoprotein (S) trimer with one re... -

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Basic information

Entry
Database: EMDB / ID: EMD-11347
TitleStructure of SARS-CoV-2 spike glycoprotein (S) trimer with one receptor binding domain (RBD) in open-state determined by subtomogram averaging
Map data
SampleSevere acute respiratory syndrome coronavirus 2:
virus
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 5.4 Å
AuthorsTuronova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C ...Turonova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C / van Zandbergen G / Laundry J / de Azevedo NTD / Mosalaganti S / Schwarz A / Covino R / Muhlebach M / Hummer G / Locker JK / Beck M
CitationJournal: Science / Year: 2020
Title: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van ...Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van Zandbergen / Jonathan Landry / Nayara Trevisan Doimo de Azevedo / Shyamal Mosalaganti / Andre Schwarz / Roberto Covino / Michael D Mühlebach / Gerhard Hummer / Jacomine Krijnse Locker / Martin Beck /
Abstract: The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo- ...The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 9, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateDec 9, 2020-
Current statusDec 9, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11347.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 128 pix.
= 340.224 Å
2.66 Å/pix.
x 128 pix.
= 340.224 Å
2.66 Å/pix.
x 128 pix.
= 340.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.658 Å
Density
Contour LevelBy AUTHOR: 0.731 / Movie #1: 0.631
Minimum - Maximum-1.0319148 - 1.9635174
Average (Standard dev.)0.0147296265 (±0.1091061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 340.224 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.6582.6582.658
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z340.224340.224340.224
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.0321.9640.015

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Supplemental data

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Additional map: Raw map of the S protein with 1 open RBD.

Fileemd_11347_additional_1.map
AnnotationRaw map of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of the of the S protein with 1 open RBD.

Fileemd_11347_half_map_1.map
AnnotationHalf map of the of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of the of the S protein with 1 open RBD.

Fileemd_11347_half_map_2.map
AnnotationHalf map of the of the S protein with 1 open RBD.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2 / Number of components: 1

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Component #1: virus, Severe acute respiratory syndrome coronavirus 2

VirusName: Severe acute respiratory syndrome coronavirus 2 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 279 K / Humidity: 100 %

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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: 3.5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 4217
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 6VXX
Chain ID: A

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