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Electron tomography of isometrically contracting insect flight muscle

by electron tomography

Movie

Orientation:

#1: Solid view (volume rendering), , Image by UCSF CHIMERA

#2: Close-up, Solid view (volume rendering), , Image by UCSF CHIMERA

#3: Simplified surface model, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1561
TitleElectron tomography of isometrically contracting insect flight muscle
MapThis is a dual axis tomogram of quick frozen, freeze This is a dual axis tomogram of quick frozen, freeze substituted, plastic embedded, thin sectioned insect flight muscle from Lethocerus sp.
SampleIsometrically contracting asynchronous insect flight muscle
Keywordsinsect, muscle, myosin, troponin, tropomyosin, actin, light chains, thin filament, thick filament, electron microscopy, image processing, isometric contraction, freezing, freeze substitution, microtomy, multivariate data analysis
AuthorsWu S, Liu J, Reedy MC, Tregear RT, Winkler H, Franzini-Armstrong C, Sasaki H, Lucaveche C, Goldman YE, Reedy MK, Taylor KA
DateDeposition: 2008-09-26, Header release: 2008-09-29, Map release: 2010-04-12, Last update: 2011-12-23
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Solid view (volume rendering), , Image by UCSF CHIMERA

#2: Close-up, Solid view (volume rendering), , Image by UCSF CHIMERA

#3: Simplified surface model, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Cite: data citing same article

Article
Citation - Primary
ArticlePLoS ONE, Vol. 5, Issue 9, Year 2010
TitleElectron tomography of cryofixed, isometrically contracting insect flight muscle reveals novel actin-myosin interactions.
AuthorsShenping Wu, Jun Liu, Mary C Reedy, Richard T Tregear, Hanspeter Winkler, Clara Franzini-Armstrong, Hiroyuki Sasaki, Carmen Lucaveche, Yale E Goldman, Michael K Reedy, Kenneth A Taylor
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America.
KeywordsActins (chemistry), Animals, Cryopreservation, Crystallography, X-Ray, Electron Microscope Tomography, Flight, Animal, Insect Proteins (chemistry), Insects (chemistry), Isometric Contraction, Models, Molecular, Muscles (chemistry), Myosins (chemistry, 3.6.4.1), Protein Binding, Protein Structure, Tertiary, Tissue Fixation
LinksDOI: 10.1371/journal.pone.0012643, PubMed: 20844746, PMC: PMC2936580
Citation - #1
ArticleJ.STRUCT.BIOL., Vol. 168, Page 485-502, Year 2009
TitleMethods for Identifying and Averaging Variable Molecular Conformations in Tomograms of Actively Contracting Insect Flight Muscle
AuthorsWu S, Liu J, Reedy MC, Tregear RT, Winkler H, Reedy MK, Taylor KA
Map
Fileemd_1561.map.gz ( map file in CCP4 format, 588001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
70 pix
6.9 A/pix
= 483. A
1344 pix
6.9 A/pix
= 11040. A
1600 pix
6.9000007440476 A/pix
= 9273.601 A

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:
Minimum - Maximum: -3296.96 - 4848.86
Average (Standard dev.): 5.83993 (532.04)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions1344160070
Origin000
Limit1343159969
Spacing1344160070
Unit CellA: 9273.6 A, B: 11040 A, C: 483 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 6.9 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z6.90000074404766.96.9
M x/y/z1344160070
origin x/y/z0.0000.0000.000
length x/y/z9273.60111040.000483.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1600134470
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3296.9594848.8645.840
Annotation DetailsThis is a dual axis tomogram of quick frozen, freeze This is a dual axis tomogram of quick frozen, freeze substituted, plastic embedded, thin sectioned insect flight muscle from Lethocerus sp.
Supplement
Images
Images
Sample
NameIsometrically contracting asynchronous insect flight muscle
Number of Components8
Oligomeric Statetissue
DetailsThis specimen is obtained from a quick frozen, isometrically contracting asynchronous insect flight muscle that has been freeze substituted, plastic embedded, and thin sectioned
Component #1: cellular-component - muscle
Scientific namemyofibril
Common Namemuscle
DetailsThe sample was enblock stained using uranyl acetate and tannic acid, and post stained with lead citrate and potassium permanganate
Oligomeric Detailsmuscle fibril
Scientific Name of SpeciesLethocerus indicus
Common Name of SpeciesWater bug
NCBI taxonomy212017
Recombinant expressionNo
Natural SourceOrgan Or Tissue: asynchronous dorsal longitudinal flight muscle
Organelle: myofibril
Cell Location: myooplasm
Experiment
Sample Preparation
StainingFreeze slammed fibers were freeze-substituted in acetone using a tannic aciduranyl acetate sequence, and ultimately embedded in Araldite-506 for thin-section electron microscopy. Ultrathin (25-30 nm) longitudinal sections were stained by permanganate-lead.
BufferDetails: 20 mM MOPS buffer, 5 mM NaN3, and MgCl2, ATP, CaCl2, and EGTA in varying millimolar concentrations
Vitrification
Methodsmash against a liquid helium cooled Au-coated Cu mirror
Cryogen NameHELIUM
DetailsVitrification instrument: modified Heuser Cryopress freezing head
InstrumentHOMEMADE PLUNGER
Temperature4.5 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Illumination ModeFLOOD BEAM
Lens
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderGatan model 670 Ultrahigh tilt analytical holder
ModelOTHER
Tilt Angle-72 degrees - 72 degrees
Camera
DetectorTVIPS TEMCAM-F224 (2k x 2k)
Image Acquisition
#1
Quant Bit Number16
DetailsImages recorded on a TVIPS Tem-Cam F224 2k x 2k CCD camera
Processing
Methodelectron tomography
3D reconstruction
Algorithmmarker free alignment
SoftwarePROTOMO, IMOD
DetailsTwo tilt series at 90 degrees to one another were first independently aligned using marker-free alignment and area matching. The two resulting tomograms were then merged by patch correlation and volume warp using IMOD. Tomogram computed using weighted back projection.
Resolution MethodFSC 0.5
Tomography
Number of Sections70
Download
Data from EMDB
Header (meta data in XML format)emd-1561.xml (8.5 KB)
Map dataemd_1561.map.gz (532.4 MB)
Images1561.gif (189 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1561
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 1.8 MB
.webm (WebM/VP8 format), 2.9 MB
Session file for UCSF-Chimera, 24.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 1.8 MB
.webm (WebM/VP8 format), 2.8 MB
Session file for UCSF-Chimera, 24.9 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 1.9 MB
.webm (WebM/VP8 format), 2.9 MB