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Conformational reorganization of the SARS coronavirus spike following receptor binding: implications for membrane fusion.

by single particle reconstruction, at 18.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0025, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0025, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1425
AuthorsBeniac DR, deVarennes SL, Andonov A, He R, Booth TF
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0025, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0025, Made by UCSF CHIMERA

Supplemental images

1425.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1423
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1423

EMDB-5144
List of similar structure data about Omokage system
Article
Citation - Primary
ArticlePLoS ONE, Vol. 2, Issue 10, Page e1082, Year 2007
TitleConformational reorganization of the SARS coronavirus spike following receptor binding: implications for membrane fusion.
AuthorsDaniel R Beniac, Shauna L deVarennes, Anton Andonov, Runtao He, Tim F Booth
Viral Diseases Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
KeywordsAnimals, Cercopithecus aethiops, Cryoelectron Microscopy, Humans, Image Processing, Computer-Assisted, Membrane Fusion, Membrane Glycoproteins (chemistry), Microscopy, Immunoelectron, Models, Molecular, Molecular Conformation, Peptidyl-Dipeptidase A (chemistry, 3.4.15.1), Protein Binding, Protein Conformation, SARS Virus (metabolism), Vero Cells, Viral Envelope Proteins (chemistry), angiotensin converting enzyme 2 (3.4.17.-), spike glycoprotein, coronavirus (107476-75-5)
LinksDOI: 10.1371/journal.pone.0001082, PubMed: 17957264, PMC: PMC2034598
Map
FileEMD-1425.map ( map file in CCP4 format, 67109 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.00349, 0.0025 (movie #1):
Minimum - Maximum: -0.010725 - 0.0251682
Average (Standard dev.): -5.59771e-06 (0.0017535)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 256 256 256
Origin : 0 0 0
Limit : 255 255 255
Spacing : 256 256 256
Unit CellA = 544 A , B = 544 A , C = 544 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 2.125 A , Y = 2.125 A , Z = 2.125 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0110.025-0.000
Annotation DetailsSARS coronavirus spike plus receptor angiotensin converting enzyme 2 (ACE2)
Supplement
Images
Images

1425.gif
Sample
NameSpike of SARS coronavirus attached to lipid envelope complexed with receptor ACE2
Number of Components2
Oligomeric Statetrimer
Detailsspike attached to virus was inactivated by gamma irradiation
Component #1: virus - S protein
Scientific nameSARS coronavirus
Common NameS protein
Theoretical Mass0.5 MDa
Experimental Mass0.5 MDa
Detailsspike attached to virus envelope
Scientific Name of SpeciesSARS coronavirus (NCBI Taxonomy: 227859)
Common Name of SpeciesS protein
EnvelopedYes
EmptyNo
ClassVIRION
IsolateSTRAIN
Natural SourceHost Category: VERTEBRATES
Host Species: Homo sapiens (NCBI Taxonomy: 9606)
Component #2: ligand - ACE2
Scientific nameAngiotensin converting enzyme 2
Common NameACE2
Theoretical Mass0.12 MDa
Experimental Mass0.12 MDa
Detailsreceptor ACE2 with part of human Fc; Note: this is a fusion protein containing 740 amino acids of the extracellular domain of ACE2 and 250 amino acids of the Fc human IGg1
Oligomeric Detailsdimer
Number of Copies2
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of Specieshuman
Recombinant expressionYes
Natural SourceCell Location: plasma membrane
Engineered SourceExp System: Homo sapiens (NCBI Taxonomy: 9606)
LinksInterPro: IPR:006025, Gene Ontology: GO:0005576
Experiment
Sample Preparation
Stainingcryo, freezee plunge
Specimen Support DetailsHoley carbon on 400 mesh Cu grids
Specimen Stateparticle
BufferDetails: 1 times phosphate buffered saline
pH: 7.4
Vitrification
Methodblot 3 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Reichert plunger
Humidity40
InstrumentREICHERT-JUNG PLUNGER
Temperature93 Kelvin
Imaging
MicroscopeFEI TECNAI 20
Date29-JUL-2006
Electron Gun
Electron SourceLAB6
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 29000 X, Calibrated: 29968 X
Nominal Cs2.0 mm
Imaging ModeBRIGHT FIELD
Defocus2900 nm - 11900 nm
Specimen Holder
HolderSide entry liquid nitrogen-coolde ( GATAN LIQUID NITROGEN )
Temperature93 Kelvin
Camera
DetectorKodak SO163
Image Acquisition
Number of Digital Images99
Sampling Size6.4 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmprojection matching
SoftwareSPIDER
CTF Correctioneach particle
Resolution By Author18.5
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages1073
Number of Projections11153
DetailsThe particles were selected manually
Download
Data from EMDB
Header (meta data in XML format)emd-1425.xml (8.7 KB)
Map dataemd_1425.map.gz (59.4 MB)
Images1425.gif (44.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1425
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.2 MB
Session file for UCSF-Chimera, 27.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 4 MB
Session file for UCSF-Chimera, 27.4 KB