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Yorodumi- PDB-8g2z: 48-nm doublet microtubule from Tetrahymena thermophila strain CU428 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g2z | ||||||
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Title | 48-nm doublet microtubule from Tetrahymena thermophila strain CU428 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Cilia / Axoneme / Doublet Microtubule / Microtubule Inner Protein | ||||||
Function / homology | Function and homology information membrane-bounded organelle / axoneme assembly / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process ...membrane-bounded organelle / axoneme assembly / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cilium / structural constituent of cytoskeleton / microtubule / hydrolase activity / phosphorylation / GTPase activity / calcium ion binding / GTP binding / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Black, C.S. / Kubo, S. / Yang, S.K. / Bui, K.H. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins. Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente- ...Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente-Paterno / Chelsea De Bellis / Phuong M Huynh / Zhe Fan / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui / Abstract: Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine ...Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g2z.cif.gz | 27.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8g2z.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8g2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/8g2z ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2z | HTTPS FTP |
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-Related structure data
Related structure data | 29685MC 8g3dC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 44 types, 425 molecules 0A1A2A3A0B0C1C0D1D2D0E1E2E3E0F0G1G0H1H0N1N2N0Q1Q2Q3Q4Q5Q6Q0T...
-Parkin co-regulated protein ... , 2 types, 6 molecules 0S1S2S3S4S5S
#11: Protein | Mass: 36304.816 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: CU428 / References: UniProt: I7MLV6 #35: Protein | Mass: 28413.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: CU428 / References: UniProt: I7M317 |
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-Non-polymers , 3 types, 483 molecules
#47: Chemical | ChemComp-GTP / #48: Chemical | ChemComp-MG / #49: Chemical | ChemComp-GDP / |
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-Details
Has ligand of interest | Y |
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Sequence details | The identities of those residues that could be observed in chains 5I, 5J, 5K, 8L, 8N, 8P and 8R ...The identities of those residues that could be observed in chains 5I, 5J, 5K, 8L, 8N, 8P and 8R could not be determined. All of the residues in chains 5I, 5J, 5K, 8L, 8N and 8P were modeled as unknown residues (UNK). The residues in chain 8R were modeled as a mixture of UNK, ALA and TYR residues. The actual sequence of OJ3 (chains 5I, 5J, and 5K) is: MADKSSQVKT |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 48-nm repeat unit of microtubule doublet from Tetrahymena thermophila strain CU428 Type: ORGANELLE OR CELLULAR COMPONENT Details: Single Particle Analysis of the 48-nm repeating unit of the axoneme from intact cilia purified from Tetrahymena strain CU428 Entity ID: #46, #45, #38, #21, #16, #27, #15, #26, #24, #28, #17, #9, #18, #29, #33, #8, #14, #22, #20, #13, #23, #19, #10, #25, #34, #4, #7, #3, #32, #41, #39-#40, #2, #30, #6, #35, #11, #36, #12, ...Entity ID: #46, #45, #38, #21, #16, #27, #15, #26, #24, #28, #17, #9, #18, #29, #33, #8, #14, #22, #20, #13, #23, #19, #10, #25, #34, #4, #7, #3, #32, #41, #39-#40, #2, #30, #6, #35, #11, #36, #12, #31, #1, #5, #37, #42-#44 Source: NATURAL |
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Molecular weight | Value: 7.6 MDa / Experimental value: YES |
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: CU428 / Organelle: Cilia |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148365 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 32 / Num. of volumes extracted: 2608 | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 191.39 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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