Journal: Curr Biol / Year: 2013 Title: Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry. Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu ...Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu Moriya / Michel O Steinmetz / Yuichi Hongoh / Pierre Gönczy / Abstract: BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel ...BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel that dictates the 9-fold symmetry of centrioles. Although the cartwheel architecture has been recently analyzed, how it connects to the peripheral microtubules is not understood. More generally, a high-resolution view of the proximal region of the centriole is lacking, thus limiting understanding of the underlying assembly mechanisms. RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the ...RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the cartwheel that exhibit a 9-fold symmetrical arrangement, as well as the structure of the Pinhead and the A-C linker that connect to microtubules. Moreover, we uncover striking chiral features that might impart directionality to the entire centriole. Furthermore, we identify Trichonympha SAS-6 and demonstrate that it localizes to the cartwheel in vivo. CONCLUSIONS: Our work provides unprecedented insight into the architecture of the centriole proximal region, which is key for a thorough understanding of the mechanisms governing centriole assembly.
History
Deposition
Mar 11, 2013
-
Header (metadata) release
Apr 10, 2013
-
Map release
Aug 21, 2013
-
Update
Sep 25, 2013
-
Current status
Sep 25, 2013
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_2330.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha.
Voxel size
X=Y=Z: 7.5 Å
Density
Contour Level
By EMDB: 0.0 / Movie #1: 0.4
Minimum - Maximum
-3.1838901 - 2.45359182
Average (Standard dev.)
-0.90669858 (±0.93229675)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
124
111
66
Spacing
124
111
66
Cell
A: 832.5 Å / B: 930.0 Å / C: 495.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
7.5
7.5
7.5
M x/y/z
111
124
66
origin x/y/z
0.000
0.000
0.000
length x/y/z
832.500
930.000
495.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-27
-15
-36
NX/NY/NZ
55
31
73
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
111
124
66
D min/max/mean
-3.184
2.454
-0.907
-
Supplemental data
-
Sample components
-
Entire : electron cryo-tomography reconstruction and subvolume averaging o...
Entire
Name: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
Components
Sample: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha
Organelle or cellular component: Basal body
-
Supramolecule #1000: electron cryo-tomography reconstruction and subvolume averaging o...
Supramolecule
Name: electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from trichonympha type: sample / ID: 1000 / Number unique components: 1
-
Supramolecule #1: Basal body
Supramolecule
Name: Basal body / type: organelle_or_cellular_component / ID: 1 / Name.synonym: centriole / Recombinant expression: No
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi