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Cryo-EM reconstruction of native and expanded Turnip Crinkle virus

by single particle (icosahedral) reconstruction, at 17 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.2, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.2, Made by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-3zx9, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1864
TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
Map3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
SampleTurnip crinkle virus
KeywordsTurnip crinkle virus, genomic RNA structure, genome uncoating, ssRNA virus
AuthorsBakker SE, Robottom J, Pearson AR, Stockley PG, Ranson NA
DateDeposition: 2011-01-25, Header release: 2012-07-09, Map release: 2012-07-09, Last update: 2012-07-09
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.2, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.2, Made by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-3zx9, Made by Jmol

Supplemental images

image1864.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3zx9
CiteFit

EMDB-1863
Cite

PDB-3zx8
Cite

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)

Diagram

EMDB-5529

EMDB-1968

EMDB-5161

EMDB-5379

EMDB-1150
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 417, Issue 1-2, Page 65-78, Year 2012
TitleIsolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus.
AuthorsSaskia E Bakker, Robert J Ford, Amy M Barker, Janice Robottom, Keith Saunders, Arwen R Pearson, Neil A Ranson, Peter G Stockley
Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
KeywordsCapsid (chemistry), Carmovirus (chemistry), Cryoelectron Microscopy, RNA, Viral (analysis), Virion
LinksPII: S0022-2836(12)00071-X, DOI: 10.1016/j.jmb.2012.01.017, PubMed: 22306464
Citation - #1
ArticleJ. Mol. Biol., Vol. 191, Issue 4, Page 625-38, Year 1986
TitleStructure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
AuthorsJ M Hogle, A Maeda, S C Harrison
KeywordsCapsid, Computer Simulation, Macromolecular Substances, Models, Biological, Plant Viruses (analysis), RNA Viruses (analysis), Viral Envelope Proteins, X-Ray Diffraction
LinksPubMed: 3806676, PII: 0022-2836(86)90450-X
Map
FileEMD-1864.map ( map file in CCP4 format, 55298 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:3.2 (by author), 3.2 (movie #1):
Minimum - Maximum: -1.86774302 - 4.17278814
Average (Standard dev.): 0.16210388 (1.48636842)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 240 240 240
Origin : 0 0 0
Limit : 239 239 239
Spacing : 240 240 240
Unit CellA = 453.6 A , B = 453.6 A , C = 453.6 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 1.89 A , Y = 1.89 A , Z = 1.89 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.891.891.89
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.8684.1730.162
Annotation Details3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
Supplement
Images
Images

image1864.png
Sample
NameTurnip crinkle virus
Number of Components1
Oligomeric StateIcosahedral virus
Theoretical Mass6.8 MDa
Component #1: virus - Turnip crinkle virus
Scientific nameTurnip crinkle virus
Theoretical Mass6.8 MDa
Scientific Name of SpeciesTurnip crinkle virus (NCBI Taxonomy: 11988)
Common Name of SpeciesTurnip crinkle virus
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceHost Species: Brassica rapa subsp. rapa (NCBI Taxonomy: 51350)
ShellDiameter: 380 A
Name Element: Expanded
T Number: 3
Experiment
Sample Preparation
Specimen Conc3 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 100 mM Tris pH 8.5, 5 mM EDTA
pH: 8.5
Vitrification
MethodBlot 1.6 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Double sided automated blotter and plunger
InstrumentHOMEMADE PLUNGER
Temperature77 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X, Calibrated: 52911 X
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3500 nm
Specimen Holder
HolderGatan 626 ( GATAN LIQUID NITROGEN )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerOTHER
Number of Digital Images41
Sampling Size10 microns
Processing
Methodsingle particle (icosahedral) reconstruction
3 D reconstruction
AlgorithmIcosahedral
SoftwareSPIDER
CTF CorrectionPhase-flipping each particle
Resolution By Author17
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections5121
Number of Class Averages110
Applied SymmetryI (icosahedral)
Fitted Coordinate
PDB entry ID

PDB-3zx9
Download
Data from EMDB
Header (meta data in XML format)emd-1864.xml (8 KB)
Map dataemd_1864.map.gz (48 MB)
Imagesimage1864.png (151.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1864
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.5 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB