- EMDB-12121: Cropped cryo-ET average map of axonemal 96nm-repeat from Tetrahym... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-12121
Title
Cropped cryo-ET average map of axonemal 96nm-repeat from Tetrahymena CCDC96-deletion mutant, which shows the structure of the N-DRC and the absence of the Ccdc113/Ccdc96 complex structure.
Map data
Cropped cryo-ET average map of axonemal 96nm-repeat from Tetrahymena CCDC96-deletion mutant, showing the N-DRC and lacking the structure of the Ccdc113/Ccdc96 complex.
Sample
Organelle or cellular component: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
Biological species
Tetrahymena thermophila (eukaryote)
Method
subtomogram averaging / cryo EM / Resolution: 34.0 Å
H2020 Marie Curie Actions of the European Commission
753954
Germany
Polish National Science Centre
2014/14/M/NZ3/00511
Poland
Polish National Science Centre
No 2016/23/N/NZ3/02420
Poland
Citation
Journal: PLoS Genet / Year: 2021 Title: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link. Authors: Rafał Bazan / Adam Schröfel / Ewa Joachimiak / Martyna Poprzeczko / Gaia Pigino / Dorota Wloga / Abstract: Ciliary beating requires the coordinated activity of numerous axonemal complexes. The protein composition and role of radial spokes (RS), nexin links (N-DRC) and dyneins (ODAs and IDAs) is well ...Ciliary beating requires the coordinated activity of numerous axonemal complexes. The protein composition and role of radial spokes (RS), nexin links (N-DRC) and dyneins (ODAs and IDAs) is well established. However, how information is transmitted from the central apparatus to the RS and across other ciliary structures remains unclear. Here, we identify a complex comprising the evolutionarily conserved proteins Ccdc96 and Ccdc113, positioned parallel to N-DRC and forming a connection between RS3, dynein g, and N-DRC. Although Ccdc96 and Ccdc113 can be transported to cilia independently, their stable docking and function requires the presence of both proteins. Deletion of either CCDC113 or CCDC96 alters cilia beating frequency, amplitude and waveform. We propose that the Ccdc113/Ccdc96 complex transmits signals from RS3 and N-DRC to dynein g and thus regulates its activity and the ciliary beat pattern.
History
Deposition
Dec 15, 2020
-
Header (metadata) release
Mar 17, 2021
-
Map release
Mar 17, 2021
-
Update
Mar 17, 2021
-
Current status
Mar 17, 2021
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_12121.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Cropped cryo-ET average map of axonemal 96nm-repeat from Tetrahymena CCDC96-deletion mutant, showing the N-DRC and lacking the structure of the Ccdc113/Ccdc96 complex.
Voxel size
X=Y=Z: 7.06 Å
Density
Contour Level
By AUTHOR: 138.0 / Movie #1: 138
Minimum - Maximum
15.401919 - 240.53255
Average (Standard dev.)
117.02704 (±26.69121)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
3
0
Dimensions
80
77
55
Spacing
77
80
55
Cell
A: 543.62 Å / B: 564.8 Å / C: 388.3 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
7.06
7.06
7.06
M x/y/z
77
80
55
origin x/y/z
0.000
0.000
0.000
length x/y/z
543.620
564.800
388.300
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
3
0
0
NC/NR/NS
77
80
55
D min/max/mean
15.402
240.533
117.027
-
Supplemental data
-
Sample components
-
Entire : Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that...
Entire
Name: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
Components
Organelle or cellular component: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link.
-
Supramolecule #1: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that...
Supramolecule
Name: Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link. type: organelle_or_cellular_component / ID: 1 / Parent: 0
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