- EMDB-11948: Axonemal 96nm-repeat from active flagella of wild type mouse, sho... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-11948
Title
Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of sub-tomograms from cryo-electron tomograms of wild type active flagella.
Map data
Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations.
Sample
Complex: Axonemal 96nm-repeat
Biological species
Mus musculus (house mouse)
Method
subtomogram averaging / cryo EM / Resolution: 30.7 Å
Journal: Science / Year: 2021 Title: Tubulin glycylation controls axonemal dynein activity, flagellar beat, and male fertility. Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis ...Authors: Sudarshan Gadadhar / Gonzalo Alvarez Viar / Jan Niklas Hansen / An Gong / Aleksandr Kostarev / Côme Ialy-Radio / Sophie Leboucher / Marjorie Whitfield / Ahmed Ziyyat / Aminata Touré / Luis Alvarez / Gaia Pigino / Carsten Janke / Abstract: Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. ...Posttranslational modifications of the microtubule cytoskeleton have emerged as key regulators of cellular functions, and their perturbations have been linked to a growing number of human pathologies. Tubulin glycylation modifies microtubules specifically in cilia and flagella, but its functional and mechanistic roles remain unclear. In this study, we generated a mouse model entirely lacking tubulin glycylation. Male mice were subfertile owing to aberrant beat patterns of their sperm flagella, which impeded the straight swimming of sperm cells. Using cryo-electron tomography, we showed that lack of glycylation caused abnormal conformations of the dynein arms within sperm axonemes, providing the structural basis for the observed dysfunction. Our findings reveal the importance of microtubule glycylation for controlled flagellar beating, directional sperm swimming, and male fertility.
History
Deposition
Nov 17, 2020
-
Header (metadata) release
Jan 20, 2021
-
Map release
Jan 20, 2021
-
Update
Jan 20, 2021
-
Current status
Jan 20, 2021
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
A: 678.384 Å / B: 1507.52 Å / C: 829.136 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
9.422
9.422
9.422
M x/y/z
72
160
88
origin x/y/z
0.000
0.000
0.000
length x/y/z
678.384
1507.520
829.136
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
43
0
46
NC/NR/NS
72
160
88
D min/max/mean
-40.844
43.066
1.053
-
Supplemental data
-
Sample components
-
Entire : Axonemal 96nm-repeat
Entire
Name: Axonemal 96nm-repeat
Components
Complex: Axonemal 96nm-repeat
-
Supramolecule #1: Axonemal 96nm-repeat
Supramolecule
Name: Axonemal 96nm-repeat / type: complex / ID: 1 / Parent: 0 Details: Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of ...Details: Axonemal 96nm-repeat from active flagella of wild type mouse, showing inner dynein arms (IDAs) in pre-power stroke conformations. Reconstruction obtained with classification and averaging of sub-tomograms from cryo-electron tomograms of wild type active flagella.
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