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- EMDB-9586: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex, ACE... -

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Basic information

Entry
Database: EMDB / ID: 9586
TitleTrypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 2
Map data
SampleTrypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
  • Trypsin-cleaved SARS-CoV spike
  • human ACE2Angiotensin-converting enzyme 2
SourceSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 9 Å resolution
AuthorsGui M / Song W
CitationJournal: PLoS Pathog. / Year: 2018
Title: Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2.
Authors: Wenfei Song / Miao Gui / Xinquan Wang / Ye Xiang
DateDeposition: Jul 26, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 22, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9586.map.gz (map file in CCP4 format, 7627 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
124 pix
2.54 Å/pix.
= 314.96 Å
124 pix
2.54 Å/pix.
= 314.96 Å
124 pix
2.54 Å/pix.
= 314.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.54 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.03449967 - 0.2340392
Average (Standard dev.)0.0042057442 (0.023431947)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions124124124
Origin0.0.0.
Limit123.123.123.
Spacing124124124
CellA=B=C: 314.96 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.542.542.54
M x/y/z124124124
origin x/y/z0.0000.0000.000
length x/y/z314.960314.960314.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS124124124
D min/max/mean-0.0340.2340.004

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Supplemental data

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Mask #1

Fileemd_9586_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex

EntireName: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
Number of components: 3

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Component #1: protein, Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex

ProteinName: Trypsin-cleaved SARS-CoV spike glycoprotein and ACE2 complex
Recombinant expression: No
MassTheoretical: 400 kDa

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Component #2: protein, Trypsin-cleaved SARS-CoV spike

ProteinName: Trypsin-cleaved SARS-CoV spike / Recombinant expression: No
SourceSpecies: SARS coronavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, human ACE2

ProteinName: human ACE2Angiotensin-converting enzyme 2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 46321
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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