Journal: Nat Commun / Year: 2017 Title: Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins. Authors: Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui Abstract: Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the ...Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule.
Average exposure time: 1.4 sec. / Electron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 4 / Number of real images: 5983
Image scans
Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7
-
Processing
EM software
ID
Name
Version
Category
1
E2helixboxer
2
PARTICLESELECTION
2
EPU
1.6
IMAGEACQUISITION
4
ctffind4
CTFCORRECTION
7
Chimera
MODELFITTING
9
PHENIX
MODELREFINEMENT
10
MATLAB
INITIALEULERASSIGNMENT
11
TomAv3
FINALEULERASSIGNMENT
13
TomAV3
RECONSTRUCTION
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Number of particles selected: 127428
Symmetry
Point symmetry: C1
3D reconstruction
Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23 Details: 23 boxes of the protofilament are boxed out from the doublet map (EMD-8528), aligned and averaged using subtomogram averaging software. Symmetry type: POINT
Atomic model building
Ref protocol: BACKBONE TRACE / Ref space: REAL / Target criteria: minimization global
+
About Yorodumi
-
News
-
Jul 12, 2017. Major update of PDB
Major update of PDB
wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
All the functionalities will be ported from the levgacy version.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi