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- EMDB-9588: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein an... -

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Basic information

Entry
Database: EMDB / ID: 9588
TitleTrypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-free conformation with three RBD in down conformation
Map data
SampleTrypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein:
Spike glycoprotein
Function / homologyCoronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell ...Coronavirus S2 glycoprotein / Spike glycoprotein N-terminal domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike glycoprotein, N-terminal / Spike receptor binding domain superfamily / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding / Spike glycoprotein
Function and homology information
SourceSARS coronavirus / Human SARS coronavirus
Methodsingle particle reconstruction / cryo EM / 3.6 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
Validation ReportPDB-ID: 6acc

SummaryFull reportAbout validation report
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: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6acc
  • Surface level: 8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9588.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:8.0 (by author), 8 (movie #1):
Minimum - Maximum-35.224930000000001 - 52.521389999999997
Average (Standard dev.)-0.000000000000563 (1.)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZYX
Dimensions288288288
Origin0.0.0.
Limit287.287.287.
Spacing288288288
CellA=B=C: 380.16 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ288288288
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-35.22552.521-0.000

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Supplemental data

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Mask #1

Fileemd_9588_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 and low pH-treated SARS-CoV spike glycoprotein

EntireName: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein
Number of components: 2

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Component #1: protein, Trypsin-cleaved and low pH-treated SARS-CoV spike glycop...

ProteinName: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein
Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: SARS coronavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 133.763422 kDa
SourceSpecies: Human SARS coronavirus
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: 5.8
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: C3 (3 fold cyclic) / Number of projections: 150269
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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