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Yorodumi- EMDB-22475: Composite cryo-EM density map of the radial spoke 1 isolated from... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22475 | |||||||||
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Title | Composite cryo-EM density map of the radial spoke 1 isolated from Chlamydomonas reinhardtii | |||||||||
Map data | composite map | |||||||||
Sample |
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Function / homology | Function and homology information radial spoke head / radial spoke / positive regulation of cilium-dependent cell motility / kinocilium / cilium movement involved in cell motility / cilium movement / motile cilium assembly / axoneme assembly / dynein complex / cytoplasmic dynein complex ...radial spoke head / radial spoke / positive regulation of cilium-dependent cell motility / kinocilium / cilium movement involved in cell motility / cilium movement / motile cilium assembly / axoneme assembly / dynein complex / cytoplasmic dynein complex / Set1C/COMPASS complex / UTP biosynthetic process / ciliary plasm / Oxidoreductases / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / dynein intermediate chain binding / axoneme / microtubule-based process / protein peptidyl-prolyl isomerization / chaperone cofactor-dependent protein refolding / centriole / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cilium / unfolded protein binding / protein folding / protein-folding chaperone binding / microtubule / calmodulin binding / oxidoreductase activity / cytoskeleton / calcium ion binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Gui M / Ma M / Sze-Tu E / Wang X / Koh F / Zhong E / Berger B / Davis J / Dutcher S / Zhang R / Brown A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structures of radial spokes and associated complexes important for ciliary motility. Authors: Miao Gui / Meisheng Ma / Erica Sze-Tu / Xiangli Wang / Fujiet Koh / Ellen D Zhong / Bonnie Berger / Joseph H Davis / Susan K Dutcher / Rui Zhang / Alan Brown / Abstract: In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two ...In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two complementary cryo-EM strategies to determine structures of the major mechanoregulators that bind ciliary doublet microtubules in Chlamydomonas reinhardtii. We determine structures of isolated radial spoke RS1 and the microtubule-bound RS1, RS2 and the nexin-dynein regulatory complex (N-DRC). From these structures, we identify and build atomic models for 30 proteins, including 23 radial-spoke subunits. We reveal how mechanoregulatory complexes dock to doublet microtubules with regular 96-nm periodicity and communicate with one another. Additionally, we observe a direct and dynamically coupled association between RS2 and the dynein motor inner dynein arm subform c (IDAc), providing a molecular basis for the control of motor activity by mechanical signals. These structures advance our understanding of the role of mechanoregulation in defining the ciliary waveform. | |||||||||
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_22475.map.gz | 21.2 MB | EMDB map data format | |
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Header (meta data) | emd-22475-v30.xml emd-22475.xml | 49.3 KB 49.3 KB | Display Display | EMDB header |
Images | emd_22475.png | 69.2 KB | ||
Masks | emd_22475_msk_1.map emd_22475_msk_2.map emd_22475_msk_3.map emd_22475_msk_4.map emd_22475_msk_5.map emd_22475_msk_6.map emd_22475_msk_7.map emd_22475_msk_8.map | 669.9 MB 669.9 MB 669.9 MB 669.9 MB 669.9 MB 669.9 MB 669.9 MB 669.9 MB | Mask map | |
Others | emd_22475_additional_1.map.gz emd_22475_additional_2.map.gz emd_22475_additional_3.map.gz emd_22475_additional_4.map.gz emd_22475_additional_5.map.gz emd_22475_additional_6.map.gz emd_22475_additional_7.map.gz emd_22475_additional_8.map.gz | 13.6 MB 22.1 MB 6.4 MB 6.9 MB 3.4 MB 2.6 MB 2.4 MB 2.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22475 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22475 | HTTPS FTP |
-Validation report
Summary document | emd_22475_validation.pdf.gz | 189.3 KB | Display | EMDB validaton report |
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Full document | emd_22475_full_validation.pdf.gz | 188.8 KB | Display | |
Data in XML | emd_22475_validation.xml.gz | 503 B | Display | |
Data in CIF | emd_22475_validation.cif.gz | 372 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22475 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22475 | HTTPS FTP |
-Related structure data
Related structure data | 7jtkMC 7jtsC 7ju4C 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_22475.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Mask #5
+Mask #6
+Mask #7
+Mask #8
+Additional map: #6
+Additional map: #5
+Additional map: #4
+Additional map: #3
+Additional map: #2
+Additional map: #8
+Additional map: #7
+Additional map: #1
-Sample components
+Entire : radial spoke 1
+Supramolecule #1: radial spoke 1
+Macromolecule #1: Flagellar radial spoke protein 1
+Macromolecule #2: Flagellar radial spoke protein 2
+Macromolecule #3: Flagellar radial spoke protein 3
+Macromolecule #4: Flagellar radial spoke protein 4
+Macromolecule #5: Flagellar radial spoke protein 5
+Macromolecule #6: Flagellar radial spoke protein 6
+Macromolecule #7: Flagellar radial spoke protein 7
+Macromolecule #8: Flagellar radial spoke protein 9
+Macromolecule #9: Flagellar radial spoke protein 10
+Macromolecule #10: Flagellar radial spoke protein 11
+Macromolecule #11: Flagellar radial spoke protein 12
+Macromolecule #12: Flagellar radial spoke protein 14
+Macromolecule #13: Flagellar radial spoke protein 16
+Macromolecule #14: Dynein 8 kDa light chain, flagellar outer arm
+Macromolecule #15: Unknown protein
+Macromolecule #16: Flagellar radial spoke protein 23
+Macromolecule #17: Cytochrome b5 heme-binding domain-containing protein
+Macromolecule #18: Uncharacterized protein
+Macromolecule #19: Predicted protein
+Macromolecule #20: PHOSPHATE ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.4 |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |