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Yorodumi- EMDB-22480: Cryo-EM density map of stalk of radial spoke 1 attached with doub... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22480 | |||||||||
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Title | Cryo-EM density map of stalk of radial spoke 1 attached with doublet microtubule from Chlamydomonas reinhardtii | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cilia / native / complex / microtubule / mechanoregulation / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information radial spoke / positive regulation of cilium-dependent cell motility / motile cilium assembly / dynein complex / cytoplasmic dynein complex / ciliary plasm / motile cilium / dynein intermediate chain binding / axoneme / microtubule-based process ...radial spoke / positive regulation of cilium-dependent cell motility / motile cilium assembly / dynein complex / cytoplasmic dynein complex / ciliary plasm / motile cilium / dynein intermediate chain binding / axoneme / microtubule-based process / enzyme regulator activity / acrosomal vesicle / calcium-mediated signaling / cilium / microtubule / cytoskeleton / calcium ion binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 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_22480.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-22480-v30.xml emd-22480.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_22480.png | 49 KB | ||
Masks | emd_22480_msk_1.map | 2.1 GB | Mask map | |
Filedesc metadata | emd-22480.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22480 | HTTPS FTP |
-Validation report
Summary document | emd_22480_validation.pdf.gz | 310.3 KB | Display | EMDB validaton report |
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Full document | emd_22480_full_validation.pdf.gz | 309.9 KB | Display | |
Data in XML | emd_22480_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_22480_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22480 | HTTPS FTP |
-Related structure data
Related structure data | 7jtsMC 7jtkC 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_22480.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_22480_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : stalk of radial spoke 1
Entire | Name: stalk of radial spoke 1 |
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Components |
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-Supramolecule #1: stalk of radial spoke 1
Supramolecule | Name: stalk of radial spoke 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-125 / Organelle: cilia |
-Macromolecule #1: Radial spoke protein 3
Macromolecule | Name: Radial spoke protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 56.856688 KDa |
Sequence | String: MVQAKAQQQL YTHAAEPKAV QQRRAKYRED ETTQTLPTAN IMFDRRVVRG NTYAARILPA DATQTQTKGP SPASTKKRTT RTLPPRTPE AVDGRRHIDI QTDVYLEELT DTVPEADTST QTDAFLDRPP TPLFVPQKTG TDAITQIENG DLFDFDFEVE P ILEVLVGK ...String: MVQAKAQQQL YTHAAEPKAV QQRRAKYRED ETTQTLPTAN IMFDRRVVRG NTYAARILPA DATQTQTKGP SPASTKKRTT RTLPPRTPE AVDGRRHIDI QTDVYLEELT DTVPEADTST QTDAFLDRPP TPLFVPQKTG TDAITQIENG DLFDFDFEVE P ILEVLVGK VLEQGLMEVL EEEELAAMRA HQEHFEQIRN AELVATQRME AAERRKLEEK ERRMQQERER VERERVVRQK VA ASAFARG YLSGIVNTVF DRLVSSGYIY DPVMREVETA FMPWLKEQAI GYLARGVVAR RVVDKLVEDA AAALAANRST LAD KAASTA ATVDAWAERQ AKMEAELQGK ELEAVRRRPT FVLRELKPAV ASADAVEAAA AELTAQAEEA ANAKWEADKA EAAE KARAE AEAAAEEQKA LLEELAATAA AEAEERGEEP PAEPPSLPDG VEPVDVEAEV AKAVEAVPKP PVKEVTDIDI LSYMM DKGA ITKDAIIQAL AVHALGDKAY TNHPAFAEAE GA UniProtKB: Uncharacterized protein |
-Macromolecule #2: Dynein 8 kDa light chain, flagellar outer arm
Macromolecule | Name: Dynein 8 kDa light chain, flagellar outer arm / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 10.336775 KDa |
Sequence | String: MASGSSKAVI KNADMSEEMQ ADAVDCATQA LEKYNIEKDI AAYIKKEFDR KHNPTWHCIV GRNFGSYVTH ETKHFIYFYL GQVAILLFK SG UniProtKB: Dynein 8 kDa light chain, flagellar outer arm |
-Macromolecule #3: FAP207
Macromolecule | Name: FAP207 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 28.41841 KDa |
Sequence | String: MPPNIPGTLT AESLRRKQGD QLWKTSDQKA QKEGPHHTVY WTTGERYQGS WKDNKKHGKG TVIYKNSDKY EGDWANDMRH GLGTLWLYR DGKYVVRYNG EWRADQPTGH GTFFADNGDT YEGEWLNGRR HGKGRAVYGG RPVDGFGGDV YEGYFENDVK C GPGTMMYA ...String: MPPNIPGTLT AESLRRKQGD QLWKTSDQKA QKEGPHHTVY WTTGERYQGS WKDNKKHGKG TVIYKNSDKY EGDWANDMRH GLGTLWLYR DGKYVVRYNG EWRADQPTGH GTFFADNGDT YEGEWLNGRR HGKGRAVYGG RPVDGFGGDV YEGYFENDVK C GPGTMMYA NGDVYEGLWA ADKKNGTGTY FYMSKGKRFD GVWADGAIKC GTYSEIHAPP PGTPGALPPC ELRNPDKVLA EA TMEASEA ATEAAARGL UniProtKB: MORN repeat-containing protein 3 |
-Macromolecule #4: FAP253
Macromolecule | Name: FAP253 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 75.037945 KDa |
Sequence | String: MSDPEAEQGE QGYEESPEEP GPGSEAPSPS RIDNGLDTII DIDPQTQHAE EGSNTAYESE QPDVISSYTG GQQEEDGEQA GNGAIDETT EEAAGEADDG GKASGFAVEV DAGTDAAAEG DLEPEPEPER PASASGEPQP TASTSRPASG AAARPASARP T SARPGSAA ...String: MSDPEAEQGE QGYEESPEEP GPGSEAPSPS RIDNGLDTII DIDPQTQHAE EGSNTAYESE QPDVISSYTG GQQEEDGEQA GNGAIDETT EEAAGEADDG GKASGFAVEV DAGTDAAAEG DLEPEPEPER PASASGEPQP TASTSRPASG AAARPASARP T SARPGSAA PRQPSASGGS RPGSGHPVNL APDSVGLAQQ QQQKSQIEVG AQAYEARGSS RPQSGGDAYG QAEEASAAAA AG RPSTSQS GSRPPPSREG VAVVPSIPED QPLAVPIHIE RYIAPGLKAI EVEVAQGPGM PHRLVRVLLD YTQCDAKPYL GGF RNKRTG AVYHHGATQT PRAPKYSEAD RKLSRETQTV KIKQHSQQTV REQATQMARP GVLLDNDYDK EVTPGRYQTA DERD EIVLR STLRIQRWVR GWLGRKRAAY LRGKKMEREA FLRDQEARAQ SEAEEHRRRE IQRRMHPRTA ADFEVLYNEL EAWRL QETR KIKEAGLAKE QEQQVLQQLL HKETKLLQTI DRLKINANQE NKEARIQHTL NEMSKPKKFA LRNGGKVDVH TPFTTR AKE LQQLYNGLNL PLLTVDERLD VLLHVKWTVK EFDCDLTREL VDLIDREADL LNRGRNPKML EGLRKRISSL FLNFIET PE FNPEAVRFQI VPMDFEAYLY EQVGKATAKA GTSVGTRTLS UniProtKB: IQ and ubiquitin-like domain-containing protein |
-Macromolecule #5: Calmodulin
Macromolecule | Name: Calmodulin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 18.317215 KDa |
Sequence | String: MAANTEQLTE EQIAEFKEAF ALFDKDGDGT ITTKELGTVM RSLGQNPTEA ELQDMISEVD ADGNGTIDFP EFLMLMARKM KETDHEDEL REAFKVFDKD GNGFISAAEL RHVMTNLGEK LSEEEVDEMI READVDGDGQ VNYEEFVRMM TSGATDDKDK K GHK UniProtKB: Calmodulin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
Details | This sample is attached with doublet microtubule |
-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 a doublet microtubule attached density in our dataset. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 143514 |
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-7jts: |