- EMDB-20631: Composite cryo-EM density map of the 48-nm repeat doublet microtu... -
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Basic information
Entry
Database: EMDB / ID: EMD-20631
Title
Composite cryo-EM density map of the 48-nm repeat doublet microtubule from Chlamydomonas reinhardtii
Map data
Composite cryo-EM density map of the 48-nm repeat doublet microtubule from Chlamydomonas reinhardtii
Sample
Complex: Doublet microtubule from wild-type Chlamydomonas reinhardtii
Protein or peptide: x 38 types
Ligand: x 3 types
Function / homology
Function and homology information
axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / outer dynein arm / membrane-bounded organelle / outer dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / establishment of protein localization to organelle ...axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / outer dynein arm / membrane-bounded organelle / outer dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / cilium organization / intracellular organelle / misfolded protein binding / negative regulation of microtubule depolymerization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / microtubule associated complex / GTP biosynthetic process / nucleoside diphosphate kinase activity / axoneme / chaperone cofactor-dependent protein refolding / mitotic cytokinesis / cilium assembly / alpha-tubulin binding / cellular response to unfolded protein / protein folding chaperone / heat shock protein binding / Hsp70 protein binding / mitotic spindle organization / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cilium / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / unfolded protein binding / mitotic cell cycle / protein refolding / microtubule / calmodulin binding / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function
: / Cilia- and flagella-associated protein 53 / : / : / ODAD1 central coiled coil region / Protein Flattop / Nucleoside diphosphate kinase 7 / Meiosis-specific nuclear structural protein 1 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 ...: / Cilia- and flagella-associated protein 53 / : / : / ODAD1 central coiled coil region / Protein Flattop / Nucleoside diphosphate kinase 7 / Meiosis-specific nuclear structural protein 1 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / RIB43A / RIB43A / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / : / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / Enkurin domain / Calmodulin-binding / Enkurin domain profile. / : / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / EF-hand domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Nucleotide-diphospho-sugar transferases / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 52 / Uncharacterized protein / Flagellar associated protein / Uncharacterized protein / Uncharacterized protein / TPH domain-containing protein / Uncharacterized protein / Uncharacterized protein / Flagellar associated protein ...Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 52 / Uncharacterized protein / Flagellar associated protein / Uncharacterized protein / Uncharacterized protein / TPH domain-containing protein / Uncharacterized protein / Uncharacterized protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Cilia- and flagella-associated protein 45 / Flagellar associated protein / Flagellar associated protein / Uncharacterized protein / Cilia- and flagella-associated protein 53 / Cilia- and flagella-associated protein 20 / Protein Flattop homolog / Flagellar associated protein / Predicted protein / Uncharacterized protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Outer dynein arm protein 1 / Nucleoside diphosphate kinase / Flagellar associated protein / Parkin-co-regulated gene product / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Outer dynein arm-docking complex protein DC3 / Protofilament ribbon protein of flagellar microtubules / Coiled-coil protein associated with protofilament ribbons Similarity search - Component
Biological species
Chlamydomonas reinhardtii (plant)
Method
single particle reconstruction / cryo EM / Resolution: 3.4 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01GM032843
United States
Citation
Journal: Cell / Year: 2019 Title: Structure of the Decorated Ciliary Doublet Microtubule. Authors: Meisheng Ma / Mihaela Stoyanova / Griffin Rademacher / Susan K Dutcher / Alan Brown / Rui Zhang / Abstract: The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility ...The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.
History
Deposition
Aug 22, 2019
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Header (metadata) release
Sep 4, 2019
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Map release
Nov 13, 2019
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Update
Dec 2, 2020
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Current status
Dec 2, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: DC1 / type: protein_or_peptide / ID: 34 / Number of copies: 2 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
pH: 7.4 / Component - Name: HMDEKP Details: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 0.5 mM EGTA, 25 mM KCl, PH 7.4
Vitrification
Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Specialist optics
Spherical aberration corrector: Microscope is equipped with a Cs corrector Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording
Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 6 / Number real images: 8314 / Average exposure time: 9.0 sec. / Average electron dose: 38.9 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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