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- EMDB-1423: Conformational reorganization of the SARS coronavirus spike follo... -

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Basic information

Entry
Database: EMDB / ID: EMD-1423
TitleConformational reorganization of the SARS coronavirus spike following receptor binding: implications for membrane fusion.
Map dataSARS coronavirus spike
Sample
  • Sample: Spike of SARS coronavirus attached to lipid envelope
  • Virus: SARS coronavirus
Biological speciesSARS coronavirus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 25.5 Å
AuthorsBeniac DR / deVarennes SL / Andonov A / He R / Booth TF
CitationJournal: PLoS One / Year: 2007
Title: Conformational reorganization of the SARS coronavirus spike following receptor binding: implications for membrane fusion.
Authors: Daniel R Beniac / Shauna L deVarennes / Anton Andonov / Runtao He / Tim F Booth /
Abstract: The SARS coronavirus (SARS-CoV) spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Previous structural studies of membrane fusion ...The SARS coronavirus (SARS-CoV) spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Previous structural studies of membrane fusion proteins have largely used crystallography of static molecular fragments, in isolation of their transmembrane domains. In this study we have produced purified, irradiated SARS-CoV virions that retain their morphology, and are fusogenic in cell culture. We used cryo-electron microscopy and image processing to investigate conformational changes that occur in the entire spike of intact virions when they bind to the viral receptor, angiotensin-converting enzyme 2 (ACE2). We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. Furthermore, our results show that receptor binding and subsequent membrane fusion are distinct steps, and that each spike can bind up to three ACE2 molecules. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis.
History
DepositionSep 12, 2007-
Header (metadata) releaseSep 13, 2007-
Map releaseNov 14, 2007-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1423.gif

Downloads & links

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Map

FileDownload / File: emd_1423.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS coronavirus spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 256 pix.
= 544. Å		2.13 Å/pix.
x 256 pix.
= 544. Å		2.13 Å/pix.
x 256 pix.
= 544. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.125 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00313 / Movie #1: 0.003
Minimum - Maximum-0.00989678 - 0.0291261
Average (Standard dev.)0.0000283902 (±0.00155036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 544 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1252.1252.125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z544.000544.000544.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0100.0290.000

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Supplemental data

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Sample components

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Entire : Spike of SARS coronavirus attached to lipid envelope

EntireName: Spike of SARS coronavirus attached to lipid envelope
Components
  • Sample: Spike of SARS coronavirus attached to lipid envelope
  • Virus: SARS coronavirus

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Supramolecule #1000: Spike of SARS coronavirus attached to lipid envelope

SupramoleculeName: Spike of SARS coronavirus attached to lipid envelope / type: sample / ID: 1000
Details: spike attached to virus was inactivated by gamma irradiation
Oligomeric state: trimer - spike / Number unique components: 1

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Supramolecule #1: SARS coronavirus

SupramoleculeName: SARS coronavirus / type: virus / ID: 1 / Name.synonym: S protein / Details: spike attached to virus envelope / NCBI-ID: 227859 / Sci species name: SARS coronavirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: S protein
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 500 KDa / Theoretical: 500 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 1 times phosphate buffered saline
StainingType: NEGATIVE / Details: cryo, freezee plunge
GridDetails: Holey carbon on 400 mesh Cu grids
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 93 K / Instrument: REICHERT-JUNG PLUNGER / Details: Vitrification instrument: Reichert plunger / Method: blot 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 93 K
DateDec 19, 2005
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 6.4 µm / Number real images: 63 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 29968 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 12.7 µm / Nominal defocus min: 3.3 µm / Nominal magnification: 29000
Sample stageSpecimen holder: Side entry liquid nitrogen-coolde / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected manually
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 8386
Final two d classificationNumber classes: 1486

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