- EMDB-20161: The central pair apparatus focusing on the C1a-e-c supercomplex e... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-20161
Title
The central pair apparatus focusing on the C1a-e-c supercomplex extracted from the cryo-electron tomography and subtomographic average of isolated Chlamydomonas fap92 mutant axoneme
Map data
The central pair apparatus focusing on the C1a-e-c supercomplex extracted from the cryo-electron tomography and subtomographic average of isolated Chlamydomonas fap92 mutant axoneme
Sample
Complex: The C1a-e-c supercomplex of central pair apparatus averaged from Chlamydomonas fap92 mutant cilia
Biological species
Chlamydomonas reinhardtii (plant)
Method
subtomogram averaging / cryo EM / Resolution: 22.0 Å
National Institutes of Health/National Institute of General Medical Sciences
R01GM083122
United States
National Institutes of Health/National Institute of General Medical Sciences
R37GM030626
United States
National Institutes of Health/National Institute of General Medical Sciences
R01GM112050
United States
National Institutes of Health/National Institute of General Medical Sciences
R35GM122574
United States
Citation
Journal: J Cell Biol / Year: 2019 Title: Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus. Authors: Gang Fu / Lei Zhao / Erin Dymek / Yuqing Hou / Kangkang Song / Nhan Phan / Zhiguo Shang / Elizabeth F Smith / George B Witman / Daniela Nicastro / Abstract: Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA ...Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA assembly usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of the CA projections are largely unknown. Here, we integrated biochemical and genetic approaches with cryo-electron tomography to compare the CA of wild-type with CA mutants. We identified a large (>2 MD) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and 3D structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating.
History
Deposition
Apr 26, 2019
-
Header (metadata) release
May 22, 2019
-
Map release
Nov 13, 2019
-
Update
Aug 12, 2020
-
Current status
Aug 12, 2020
Processing site: RCSB / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_20161.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
The central pair apparatus focusing on the C1a-e-c supercomplex extracted from the cryo-electron tomography and subtomographic average of isolated Chlamydomonas fap92 mutant axoneme
Voxel size
X=Y=Z: 5.523 Å
Density
Contour Level
By AUTHOR: 118 / Movie #1: 118
Minimum - Maximum
108.80237 - 128.01767
Average (Standard dev.)
116.49958 (±3.0013127)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-19
-102
-19
Dimensions
90
90
120
Spacing
90
90
120
Cell
A: 497.06998 Å / B: 497.06998 Å / C: 662.75995 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
5.523
5.523
5.523
M x/y/z
90
90
120
origin x/y/z
0.000
0.000
0.000
length x/y/z
497.070
497.070
662.760
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
254
265
109
MAP C/R/S
1
2
3
start NC/NR/NS
-102
-19
-19
NC/NR/NS
90
90
120
D min/max/mean
108.802
128.018
116.500
-
Supplemental data
-
Sample components
-
Entire : The C1a-e-c supercomplex of central pair apparatus averaged from ...
Entire
Name: The C1a-e-c supercomplex of central pair apparatus averaged from Chlamydomonas fap92 mutant cilia
Components
Complex: The C1a-e-c supercomplex of central pair apparatus averaged from Chlamydomonas fap92 mutant cilia
-
Supramolecule #1: The C1a-e-c supercomplex of central pair apparatus averaged from ...
Supramolecule
Name: The C1a-e-c supercomplex of central pair apparatus averaged from Chlamydomonas fap92 mutant cilia type: complex / 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