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Yorodumi- EMDB-22481: Composite cryo-EM density map of radial spoke 2 stalk, IDAc, and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22481 | |||||||||
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Title | Composite cryo-EM density map of radial spoke 2 stalk, IDAc, and N-DRC attached with doublet microtubule | |||||||||
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Sample |
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Keywords | cilia / native / complex / microtubule / mechanoregulation / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information regulation of cilium movement / inner dynein arm / axonemal dynein complex assembly / epithelial cilium movement involved in determination of left/right asymmetry / inner dynein arm assembly / axonemal dynein complex / cilium-dependent cell motility / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement ...regulation of cilium movement / inner dynein arm / axonemal dynein complex assembly / epithelial cilium movement involved in determination of left/right asymmetry / inner dynein arm assembly / axonemal dynein complex / cilium-dependent cell motility / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement / motile cilium assembly / axoneme assembly / dynein heavy chain binding / flagellated sperm motility / dynein complex / cytoplasmic dynein complex / ciliary plasm / motile cilium / dynein intermediate chain binding / axoneme / microtubule-based process / centriole / GTPase activator activity / acrosomal vesicle / filopodium / cell projection / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cilium / structural constituent of cytoskeleton / small GTPase binding / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / cytoskeleton / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / Golgi apparatus / extracellular region / ATP binding / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_22481.map.gz | 67.8 MB | EMDB map data format | |
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Header (meta data) | emd-22481-v30.xml emd-22481.xml | 46.5 KB 46.5 KB | Display Display | EMDB header |
Images | emd_22481.png | 143.3 KB | ||
Masks | emd_22481_msk_1.map emd_22481_msk_2.map emd_22481_msk_3.map emd_22481_msk_4.map | 2.1 GB 2.1 GB 2.1 GB 2.1 GB | Mask map | |
Filedesc metadata | emd-22481.cif.gz | 12.7 KB | ||
Others | emd_22481_additional_1.map.gz emd_22481_additional_2.map.gz emd_22481_additional_3.map.gz emd_22481_additional_4.map.gz | 4.7 MB 3.9 MB 55.8 MB 62.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22481 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22481 | HTTPS FTP |
-Related structure data
Related structure data | 7ju4MC 7jtkC 7jtsC 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_22481.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.403 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22481_msk_1.map | ||||||||||||
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-Mask #2
File | emd_22481_msk_2.map | ||||||||||||
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-Mask #3
File | emd_22481_msk_3.map | ||||||||||||
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-Mask #4
File | emd_22481_msk_4.map | ||||||||||||
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-Additional map: #1
File | emd_22481_additional_1.map | ||||||||||||
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-Additional map: #3
File | emd_22481_additional_2.map | ||||||||||||
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-Additional map: #4
File | emd_22481_additional_3.map | ||||||||||||
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-Additional map: #2
File | emd_22481_additional_4.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Complex of radial spoke 2 stalk, IDAc, and N-DRC attached with do...
+Supramolecule #1: Complex of radial spoke 2 stalk, IDAc, and N-DRC attached with do...
+Macromolecule #1: Dynein regulatory complex subunit 4
+Macromolecule #2: Dynein regulatory complex protein 1
+Macromolecule #3: Dynein regulatory complex subunit 2
+Macromolecule #4: Unknown protein
+Macromolecule #5: Tubulin beta
+Macromolecule #6: Tubulin alpha
+Macromolecule #7: Flagellar-associated protein 59
+Macromolecule #8: Flagellar-associated protein 172
+Macromolecule #9: Radial spoke protein 3
+Macromolecule #10: Radial spoke protein 7
+Macromolecule #11: Radial spoke protein 11
+Macromolecule #12: Dynein 8 kDa light chain, flagellar outer arm
+Macromolecule #13: Radial spoke protein 15
+Macromolecule #14: FAP207
+Macromolecule #15: Radial spike protein 8
+Macromolecule #16: FAP253
+Macromolecule #17: Actin
+Macromolecule #18: 28 kDa inner dynein arm light chain, axonemal
+Macromolecule #19: CFAP91 domain-containing protein
+Macromolecule #20: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #21: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Average exposure time: 9.0 sec. / Average electron dose: 38.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: Initial model was extracted from the doublet microtubule attached density in our dataset |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 202168 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-7ju4: |