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- EMDB-6705: Prefusion structure of SARS-CoV spike glycoprotein, conformation 2 -

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Basic information

Entry
Database: EMDB / ID: 6705
TitlePrefusion structure of SARS-CoV spike glycoprotein, conformation 2
SampleSARS-CoV spike trimer
SourceSARS coronavirus BJ01 / virus
Map data
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsYuan Y / Cao D
CitationNat Commun, 2017, 8, 15092-15092

Nat Commun, 2017, 8, 15092-15092 StrPapers
Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao

Validation ReportPDB-ID: 5x5b

SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: May 24, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0407
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0407
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5x5b
  • Surface level: 0.0407
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6705.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.3 Å/pix.
= 260. Å
200 pix
1.3 Å/pix.
= 260. Å
200 pix
1.3 Å/pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.0407 (by author), 0.0407 (movie #1):
Minimum - Maximum-0.11192558 - 0.2065232
Average (Standard dev.)0.00081163616 (0.0066870456)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 260 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z260.000260.000260.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.1120.2070.001

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Supplemental data

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Sample components

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Entire SARS-CoV spike trimer

EntireName: SARS-CoV spike trimer / Number of components: 2

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Component #1: protein, SARS-CoV spike trimer

ProteinName: SARS-CoV spike trimer / Recombinant expression: No
SourceSpecies: SARS coronavirus BJ01 / virus / Strain: BJ01
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Recombinant expression: No
MassTheoretical: 136.825891 kDa
Source (engineered)Expression System: SARS coronavirus BJ01 / virus / Strain: BJ01

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
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: 8 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 / Number of projections: 60000
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 2AJF, 5X4S
Chain ID: 2AJF_E, 5X4S_A
Output model

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