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Cryo-electron tomography averaged map of microtubule doublet 6 in the distal/central region of Chlamydomonas axoneme

by subtomogram averaging, at 45.7 A resolution

Movie

Orientation:

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

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2121
TitleCryo-electron tomography averaged map of microtubule doublet 6 in the distal/central region of Chlamydomonas axoneme
MapReconstruction of outer doublet 6 of the Chlamydomonas axoneme in the distal/central region.
SampleOuter doublet 6 of Chlamydomonas axoneme in the distal/central region
Keywordsaxoneme, dynein, Chlamydomonas, microtubule doublet
AuthorsBui KH, Yagi T, Yamamoto R, Kamiya R, Ishikawa T
DateDeposition: 2012-06-11, Header release: 2012-06-14, Map release: 2012-09-12, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Cell Biol., Vol. 198, Issue 5, Page 913-25, Year 2012
TitlePolarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme.
AuthorsKhanh Huy Bui, Toshiki Yagi, Ryosuke Yamamoto, Ritsu Kamiya, Takashi Ishikawa
Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland.
KeywordsChlamydomonas (chemistry), Dyneins (chemistry, 3.6.4.2), Flagella (chemistry), Microtubules (chemistry), Plant Cells (chemistry), Plant Proteins (chemistry)
LinksDOI: 10.1083/jcb.201201120, PubMed: 22945936, PMC: PMC3432765
Map
Fileemd_2121.map.gz ( map file in CCP4 format, 31251 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
7.25 A/pix
= 1450. A
200 pix
7.25 A/pix
= 1450. A
200 pix
7.25 A/pix
= 1450. 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: -6.12079477 - 9.21679306
Average (Standard dev.): 8E-8 (1.00000012)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
Unit CellA= B= C: 1450 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 7.25 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z7.257.257.25
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1450.0001450.0001450.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-6.1219.2170.000
Annotation DetailsReconstruction of outer doublet 6 of the Chlamydomonas axoneme in the distal/central region.
Supplement
Images
Images
Sample
NameOuter doublet 6 of Chlamydomonas axoneme in the distal/central region
Number of Components1
DetailsFlagella were isolated from Chlamydomonas.
Component #1: cellular-component - axoneme,cilia
Scientific nameflagellum
Common Nameaxoneme,cilia
Scientific Name of SpeciesChlamydomonas reinhardtii
Common Name of Speciesgreen algae
NCBI taxonomy3055
Strainc137 (mt+)
Recombinant expressionNo
Natural SourceOrganelle: flagella
Cell Location: distal part of the flagellum
Experiment
Sample Preparation
Specimen Conc2 mg/ml
Specimen Support Details300 mesh Quantifoil Holey Carbon copper grid R2/1
BufferDetails: 30 mM Hepes, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, and 0.5% (wt/vol) polyethylene glycol (MW 20,000)
pH: 7.4
Vitrification
MethodOffset -3, blot 3 seconds, drain time 0 second
Cryogen NameETHANE
Humidity90
InstrumentFEI VITROBOT MARK II
Temperature110 Kelvin
Imaging
MicroscopeFEI TECNAI 20
Date26-NOV-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose60 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 27500, Calibrated: 19303
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus4000 nm - 6000 nm
Energy FilterEnergy Filter: Gatan Tridem , Energy Window: 0-20 eV
Specimen Holder
HolderGatan 626, liquid nitrogen cooled
ModelGATAN LIQUID NITROGEN
Tilt Angle-60 degrees - 60 degrees
Temperature98 K ( 93 - 118 K)
Camera
DetectorGATAN ULTRASCAN 1000 (2k x 2k)
Image Acquisition
Number of Digital Images536
Quant Bit Number16
Processing
Methodsubtomogram averaging
3D reconstruction
Algorithmsubtomogram averaging
SoftwareIMOD, BSOFT, SPIDER, TOM, package, Matlab
Resolution By Author45.7 A
Resolution MethodFSC 0.5
Subtomogram Averaging
DetailsR-weighted back projection using IMOD with fiducial markers. Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2.
Download
Data from EMDB
Header (meta data in XML format)emd-2121.xml (7.7 KB)
Map dataemd_2121.map.gz (25.2 MB)
Imagesemd_2121.png (189.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2121
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, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.8 KB