+Open data
-Basic information
Entry | Database: PDB / ID: 5ubq | ||||||
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Title | Cryo-EM structure of ciliary microtubule doublet | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / cilia / doublet / axoneme / tubulin | ||||||
Function / homology | Function and homology information structural constituent of cytoskeleton / microtubule cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | ||||||
Authors | Ichikawa, M. / Liu, D. / Kastritis, P.L. / Basu, K. / Bui, K.H. | ||||||
Funding support | Canada, 1items
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Citation | 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ubq.cif.gz | 534.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ubq.ent.gz | 440.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ubq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ubq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5ubq_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5ubq_validation.xml.gz | 120.6 KB | Display | |
Data in CIF | 5ubq_validation.cif.gz | 169.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubq ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubq | HTTPS FTP |
-Related structure data
Related structure data | 8528MC 8532C 8537C 8539C 5ucyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: C1 (asymmetric)) |
-Components
#1: Protein | Mass: 48788.254 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41351 #2: Protein | Mass: 48009.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41352 #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 8nm-repeat tubulin lattice of microtubule doublet / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Cellular location: cilia / Organelle: cilia |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 3 for 5 seconds |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.4 sec. / Electron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 5983 |
Image scans | Movie frames/image: 7 / Used frames/image: 1-7 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 127429 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127429 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |