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- EMDB-7040: Tectonic conformational changes of a coronavirus spike glycoprote... -

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Basic information

Entry
Database: EMDB / ID: 7040
TitleTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
SampleMouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
SourceMurine hepatitis virus / virus / マウス肝炎ウイルス
Map dataTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Methodsingle particle reconstruction, at 4.1 Å resolution
AuthorsWalls AC / Tortorici MA
CitationProc.Natl.Acad.Sci.Usa, 2017

Proc.Natl.Acad.Sci.Usa, 2017
Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Walls AC / Tortorici MA / Snijder J / Xiong X / Bosch BJ / Rey FA / Veesler D

Validation ReportPDB-ID: 6b3o

SummaryFull reportAbout validation report
DateDeposition: Sep 22, 2017 / Header (metadata) release: Oct 4, 2017 / Map release: Oct 4, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.16
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6b3o
  • Surface level: 0.16
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_7040.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.36 Å/pix.
= 435.2 Å
320 pix
1.36 Å/pix.
= 435.2 Å
320 pix
1.36 Å/pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour Level:0.16 (by author), 0.16 (movie #1):
Minimum - Maximum-0.5127941 - 0.7845471
Average (Standard dev.)0.00019818555 (0.008341526)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.5130.7850.000

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Supplemental data

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Sample components

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Entire Mouse hepatitis virus spike glycoprotein (S2 subunit) in the post...

EntireName: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
Number of components: 2
MassTheoretical: 180 kDa

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Component #1: protein, Mouse hepatitis virus spike glycoprotein (S2 subunit) in...

ProteinName: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
Recombinant expression: No
MassTheoretical: 180 kDa
SourceSpecies: Murine hepatitis virus / virus / マウス肝炎ウイルス
Source (engineered)Expression System: Drosophila melanogaster / arthropod / キイロショウジョウバエ /

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Recombinant expression: No
MassTheoretical: 66.199094 kDa
Source (engineered)Expression System: Murine coronavirus / virus / Strain: A59

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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: 60 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: C3 (3 fold cyclic) / Number of projections: 106000
3D reconstructionSoftware: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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