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- EMDB-9595: Trypsin-cleaved SARS-CoV spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-9595
TitleTrypsin-cleaved SARS-CoV spike glycoprotein
Map data
Sample
  • Complex: Trypsin-cleaved SARS-CoV spike glycoprotein
Biological speciesSARS coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
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 /
Abstract: The trimeric SARS coronavirus (SARS-CoV) surface spike (S) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediates fusion ...The trimeric SARS coronavirus (SARS-CoV) surface spike (S) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediates fusion of the viral and cellular membranes through a pre- to postfusion conformation transition. Here, we report the structure of the SARS-CoV S glycoprotein in complex with its host cell receptor ACE2 revealed by cryo-electron microscopy (cryo-EM). The complex structure shows that only one receptor-binding domain of the trimeric S glycoprotein binds ACE2 and adopts a protruding "up" conformation. In addition, we studied the structures of the SARS-CoV S glycoprotein and its complexes with ACE2 in different in vitro conditions, which may mimic different conformational states of the S glycoprotein during virus entry. Disassociation of the S1-ACE2 complex from some of the prefusion spikes was observed and characterized. We also characterized the rosette-like structures of the clustered SARS-CoV S2 trimers in the postfusion state observed on electron micrographs. Structural comparisons suggested that the SARS-CoV S glycoprotein retains a prefusion architecture after trypsin cleavage into the S1 and S2 subunits and acidic pH treatment. However, binding to the receptor opens up the receptor-binding domain of S1, which could promote the release of the S1-ACE2 complex and S1 monomers from the prefusion spike and trigger the pre- to postfusion conformational transition.
History
DepositionJul 26, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateAug 22, 2018-
Current statusAug 22, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9595.png

Downloads & links

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Map

FileDownload / File: emd_9595.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.06050112 - 0.38384086
Average (Standard dev.)0.0036054896 (±0.023348805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions124124124
Spacing124124124
CellA=B=C: 314.96 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ288288288
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS124124124
D min/max/mean-0.0610.3840.004

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Supplemental data

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Mask #1

Fileemd_9595_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trypsin-cleaved SARS-CoV spike glycoprotein

EntireName: Trypsin-cleaved SARS-CoV spike glycoprotein
Components
  • Complex: Trypsin-cleaved SARS-CoV spike glycoprotein

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Supramolecule #1: Trypsin-cleaved SARS-CoV spike glycoprotein

SupramoleculeName: Trypsin-cleaved SARS-CoV spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: SARS coronavirus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 29848
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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