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- EMDB-6704: Prefusion structure of MERS-CoV spike glycoprotein, three-fold sy... -

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Basic information

Entry
Database: EMDB / ID: 6704
TitlePrefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry
SampleMERS-CoV spike trimer
SourceMiddle East respiratory syndrome coronavirus / virus
Map data
Methodsingle particle reconstruction, at 3.7 A 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

DateDeposition: Feb 15, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Feb 15, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5x59
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
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Supplemental images

Downloads & links

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Map

Fileemd_6704.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 A/pix
= 332.8 A
256 pix
1.3 A/pix
= 332.8 A
256 pix
1.3 A/pix
= 332.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 A
Density
Contour Level:0.0615 (by author), 0.0615 (movie #1):
Minimum - Maximum-0.23481733 - 0.4019932
Average (Standard dev.)3.0789917E-5 (0.011461312)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 332.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.2350.4020.000

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Supplemental data

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Sample components

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Entire MERS-CoV spike trimer

EntireName: MERS-CoV spike trimer / Number of components: 3

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Component #1: protein, MERS-CoV spike trimer

ProteinName: MERS-CoV spike trimer / Recombinant expression: No
SourceSpecies: Middle East respiratory syndrome coronavirus / virus
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #2: protein, S protein

ProteinName: S protein / Recombinant expression: No
MassTheoretical: 145.856203 kDa
Source (engineered)Expression System: Middle East respiratory syndrome coronavirus / virus

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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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

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/A2 / 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 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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