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Epsilon15 asymmetric reconstruction using conventional cryo-EM

by single particle reconstruction, at 13 A resolution

Movie

Orientation:

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

#2: Surface view colored by radius, Surface level: 1, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5209
TitleEpsilon15 asymmetric reconstruction using conventional cryo-EM
Mapasymmetric reconstruction of epsilon15 from conventional cryoEM particles
SampleEpsilon15
KeywordsElectron microscopy, phase plate, Bacteriophage, epsilon15
AuthorsMurata K, Liu X, Danev R, Jakana J, Schmid MF, King J, Nagayama K, Chiu W
DateDeposition: 2010-07-01, Header release: 2010-07-19, Map release: 2010-09-01, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

#2: Surface view colored by radius, Surface level: 1, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleStructure, Vol. 18, Issue 8, Page 903-12, Year 2010
TitleZernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions.
AuthorsKazuyoshi Murata, Xiangan Liu, Radostin Danev, Joanita Jakana, Michael F Schmid, Jonathan King, Kuniaki Nagayama, Wah Chiu
National Center for Macromolecular Imaging, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
KeywordsBacteriophages (ultrastructure), Bacteriorhodopsins (ultrastructure, 53026-44-1), Cryoelectron Microscopy (methods), Crystallography (methods), Electron Microscope Tomography (methods), Epsilonproteobacteria (virology), Image Processing, Computer-Assisted (methods), Microscopy, Phase-Contrast (methods), Models, Molecular
LinksPII: S0969-2126(10)00235-2, DOI: 10.1016/j.str.2010.06.006, PubMed: 20696391, PMC: PMC2925294
Map
Fileemd_5209.map.gz ( map file in CCP4 format, 746497 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
576 pix
1.95 A/pix
= 1123.2 A
576 pix
1.95 A/pix
= 1123.2 A
576 pix
1.95 A/pix
= 1123.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum: -1.46255 - 3.10983
Average (Standard dev.): 0.0642926 (0.252498)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions576576576
Origin-288-288-288
Limit287287287
Spacing576576576
Unit CellA= B= C: 1123.2 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.95 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.951.951.95
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z1123.2001123.2001123.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-288-288-288
NC/NR/NS576576576
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.4633.1100.064
Annotation Detailsasymmetric reconstruction of epsilon15 from conventional cryoEM particles
Supplement
Images
Images
Sample
NameEpsilon15
Number of Components6
Theoretical Mass0.5MDa
DetailsThe sample was monodisperse
Component #1: virus - bacteriophage
Scientific nameepsilon15
Common Namebacteriophage
Scientific Name of Speciesepsilon15
Common Name of Speciesbacteriophage
EmptyNo
EnvelopedNo
IsolateSTRAIN
ClassVIRION
Natural SourceNCBI taxonomy: 590
Host Species: Salmonella
Host Category: BACTERIA(EUBACTERIA)
ShellID: 1 , Diameter: 700 A, T Number: 7
Experiment
Sample Preparation
Specimen Support DetailsQuantifoil R2/2 grid
Specimen Stateparticle
BufferDetails: 10 mM Tris pH7.5, 25 mM NaCl and 5 mM MgCl2
pH: 7.5
Vitrification
MethodBlot for 2 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: vitrobot
InstrumentFEI VITROBOT
Imaging
MicroscopeJEOL 2200FS
Date01-DEC-2009
DetailsWeak beam illumination
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 75000, Calibrated: 75000
Nominal Cs4.3 mm
Imaging ModeBRIGHT FIELD
Energy FilterEnergy Filter: JEOL , Energy Window: 0-20 eV
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature90 K
Camera
DetectorGENERIC TVIPS (4k x 4k)
Image Acquisition
#1
Number of Digital Images722
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCross-common lines
SoftwareMPSA
CTF Correctioneach micrograph
Detailsthe map was reconstructed with ctf correction.
Resolution By Author13 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections17800
DetailsThe particles were selected using the consistency criterion of MPSA
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-5209.xml (7.3 KB)
Map dataemd_5209.map.gz (97.7 MB)
Imagesemd=5209_1.png (317.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5209
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.4 KB