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- EMDB-6682: SARS-CoV Spike Conformation 4 -

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Basic information

Entry
Database: EMDB / ID: 6682
TitleSARS-CoV Spike Conformation 4
SampleSARS-CoV spike glycoprotein
SourceSARS coronavirus / virus
Map dataSARS-CoV Spike conformation 4
Methodsingle particle reconstruction, at 6.8 Å resolution
AuthorsGui M / Song W / Xiang Y / Wang X
CitationCell Res., 2017, 27, 119-129

Cell Res., 2017, 27, 119-129 StrPapers
Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding.
Miao Gui / Wenfei Song / Haixia Zhou / Jingwei Xu / Silian Chen / Ye Xiang / Xinquan Wang

DateDeposition: Dec 1, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Dec 1, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6682.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.32 Å/pix.
= 380.16 Å
288 pix
1.32 Å/pix.
= 380.16 Å
288 pix
1.32 Å/pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.025090817 - 0.07843798
Average (Standard dev.)0.00025999543 (0.0027324033)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin000
Limit287287287
Spacing288288288
CellA=B=C: 380.16 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.321.321.32
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0250.0780.000

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Supplemental data

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Sample components

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Entire SARS-CoV spike glycoprotein

EntireName: SARS-CoV spike glycoprotein / Number of components: 1
MassTheoretical: 400 kDa

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Component #1: protein, SARS-CoV spike glycoprotein

ProteinName: SARS-CoV spike glycoprotein / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: SARS coronavirus / virus
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Vector: pFastBac-Dual

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.2
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: 4.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 38804
3D reconstructionSoftware: RELION / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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