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- EMDB-9598: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein an... -

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Basic information

Entry
Database: EMDB / ID: EMD-9598
TitleTrypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, dissociated S1-ACE2
Map data
Sample
  • Complex: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, dissociated S1-ACE2
    • Complex: S1 subunit of trypsin-cleaved and low pH-treated SARS-CoV spike
    • Complex: human ACE2
Biological speciesSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.6 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: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9598.png

Downloads & links

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Map

FileDownload / File: emd_9598.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.64 Å/pix.
x 88 pix.
= 232.32 Å		2.64 Å/pix.
x 88 pix.
= 232.32 Å		2.64 Å/pix.
x 88 pix.
= 232.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07826328 - 0.28905016
Average (Standard dev.)-0.0002498506 (±0.016553307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions888888
Spacing888888
CellA=B=C: 232.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z888888
origin x/y/z0.0000.0000.000
length x/y/z232.320232.320232.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ288288288
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS888888
D min/max/mean-0.0780.289-0.000

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Supplemental data

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Sample components

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

EntireName: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, dissociated S1-ACE2
Components
  • Complex: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, dissociated S1-ACE2
    • Complex: S1 subunit of trypsin-cleaved and low pH-treated SARS-CoV spike
    • Complex: human ACE2

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Supramolecule #1: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein an...

SupramoleculeName: Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, dissociated S1-ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: S1 subunit of trypsin-cleaved and low pH-treated SARS-CoV spike

SupramoleculeName: S1 subunit of trypsin-cleaved and low pH-treated SARS-CoV spike
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: SARS coronavirus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: human ACE2

SupramoleculeName: human ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
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: 5.8
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 41289
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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