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Yorodumi- EMDB-22446: Chlamydomonas reinhardtii radial spoke head and neck (recombinant) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22446 | ||||||||||||
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Title | Chlamydomonas reinhardtii radial spoke head and neck (recombinant) | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information radial spoke head / radial spoke / positive regulation of cilium-dependent cell motility / cilium movement involved in cell motility / motile cilium assembly / axoneme assembly / Set1C/COMPASS complex / UTP biosynthetic process / CTP biosynthetic process / Oxidoreductases ...radial spoke head / radial spoke / positive regulation of cilium-dependent cell motility / cilium movement involved in cell motility / motile cilium assembly / axoneme assembly / Set1C/COMPASS complex / UTP biosynthetic process / CTP biosynthetic process / Oxidoreductases / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / axoneme / cilium assembly / oxidoreductase activity / cytoskeleton / calmodulin binding / phosphorylation / membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||||||||
Authors | Grossman-Haham I / Coudray N / Yu Z / Wang F / Zhang N / Bhabha G / Vale RD | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structure of the radial spoke head and insights into its role in mechanoregulation of ciliary beating. Authors: Iris Grossman-Haham / Nicolas Coudray / Zanlin Yu / Feng Wang / Nan Zhang / Gira Bhabha / Ronald D Vale / Abstract: Motile cilia power cell locomotion and drive extracellular fluid flow by propagating bending waves from their base to tip. The coordinated bending of cilia requires mechanoregulation by the radial ...Motile cilia power cell locomotion and drive extracellular fluid flow by propagating bending waves from their base to tip. The coordinated bending of cilia requires mechanoregulation by the radial spoke (RS) protein complexes and the microtubule central pair (CP). Despite their importance for ciliary motility across eukaryotes, the molecular function of the RSs is unknown. Here, we reconstituted the Chlamydomonas reinhardtii RS head that abuts the CP and determined its structure using single-particle cryo-EM to 3.1-Å resolution, revealing a flat, negatively charged surface supported by a rigid core of tightly intertwined proteins. Mutations in this core, corresponding to those involved in human ciliopathies, compromised the stability of the recombinant complex, providing a molecular basis for disease. Partially reversing the negative charge on the RS surface impaired motility in C. reinhardtii. We propose that the RS-head architecture is well-suited for mechanoregulation of ciliary beating through physical collisions with the CP. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22446.map.gz | 556.3 MB | EMDB map data format | |
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Header (meta data) | emd-22446-v30.xml emd-22446.xml | 43.8 KB 43.8 KB | Display Display | EMDB header |
Images | emd_22446.png | 98.3 KB | ||
Others | emd_22446_additional_1.map.gz emd_22446_additional_2.map.gz emd_22446_additional_3.map.gz emd_22446_additional_4.map.gz emd_22446_additional_5.map.gz emd_22446_additional_6.map.gz | 551.9 MB 553.2 MB 554.7 MB 551.2 MB 552.9 MB 562.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22446 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22446 | HTTPS FTP |
-Related structure data
Related structure data | 7jrjMC 7jr9C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22446.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Focused map for the RSP1 protrusion
File | emd_22446_additional_1.map | ||||||||||||
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Annotation | Focused map for the RSP1 protrusion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map for the RSP3 protrusion
File | emd_22446_additional_2.map | ||||||||||||
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Annotation | Focused map for the RSP3 protrusion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map for the RSP2 protrusion
File | emd_22446_additional_3.map | ||||||||||||
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Annotation | Focused map for the RSP2 protrusion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map for the RSP10 protrusion
File | emd_22446_additional_4.map | ||||||||||||
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Annotation | Focused map for the RSP10 protrusion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused map for the radial spoke arm region
File | emd_22446_additional_5.map | ||||||||||||
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Annotation | Focused map for the radial spoke arm region | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: composite map
File | emd_22446_additional_6.map | ||||||||||||
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Annotation | composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Chlamydomonas reinhardtii radial spoke head and neck
+Supramolecule #1: Chlamydomonas reinhardtii radial spoke head and neck
+Macromolecule #1: Radial spoke protein 10
+Macromolecule #2: Flagellar radial spoke protein 1
+Macromolecule #3: Nucleoside diphosphate kinase 6
+Macromolecule #4: Flagellar radial spoke protein 2
+Macromolecule #5: unknown protein
+Macromolecule #6: Flagellar radial spoke protein 3
+Macromolecule #7: Flagellar radial spoke protein 5
+Macromolecule #8: Radial spoke protein 9
+Macromolecule #9: Flagellar radial spoke protein 4
+Macromolecule #10: Flagellar radial spoke protein 6
+Macromolecule #11: Flagellar radial spoke protein 6
+Macromolecule #12: Flagellar radial spoke protein 10
+Macromolecule #13: Flagellar radial spoke protein 1
+Macromolecule #14: Flagellar radial spoke protein 2
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 / Details: 30 mM HEPES, 300 mM NaCl, 1 mM TCEP |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 7572 / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 942591 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: INSILICO MODEL In silico model: A model for radial spoke protein 23 (chain K) was generated in Phyre2. The rest was built de-novo. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.9) |
Final 3D classification | Number classes: 8 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 136659 |