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Yorodumi- PDB-7jrj: Chlamydomonas reinhardtii radial spoke head and neck (recombinant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jrj | ||||||||||||
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Title | Chlamydomonas reinhardtii radial spoke head and neck (recombinant) | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Cilia / Radial spoke / Mechano-regulation | ||||||||||||
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 / motile cilium assembly / axoneme assembly / Set1C/COMPASS complex / UTP biosynthetic process / Oxidoreductases ...radial spoke head / radial spoke / positive regulation of cilium-dependent cell motility / kinocilium / cilium movement involved in cell motility / motile cilium assembly / axoneme assembly / Set1C/COMPASS complex / UTP biosynthetic process / Oxidoreductases / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / axoneme / calmodulin binding / oxidoreductase activity / cytoskeleton / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||||||||
Authors | Grossman-Haham, I. / Coudray, N. / Yu, Z. / Wang, F. / Zhang, N. / Bhabha, G. / Vale, R.D. | ||||||||||||
Funding support | United States, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jrj.cif.gz | 543.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jrj.ent.gz | 431.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jrj_validation.pdf.gz | 919.9 KB | Display | wwPDB validaton report |
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Full document | 7jrj_full_validation.pdf.gz | 939.8 KB | Display | |
Data in XML | 7jrj_validation.xml.gz | 76 KB | Display | |
Data in CIF | 7jrj_validation.cif.gz | 118.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jrj ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jrj | HTTPS FTP |
-Related structure data
Related structure data | 22446MC 7jr9C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Radial spoke protein ... , 2 types, 3 molecules EAB
#1: Protein | Mass: 23553.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP10, CHLRE_01g005450v5, CHLREDRAFT_185792 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27YU4 |
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#8: Protein | Mass: 29572.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP9, CHLRE_07g330200v5, CHLREDRAFT_182960 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27YU5 |
-Flagellar radial spoke protein ... , 10 types, 10 molecules FIGHCDLMNO
#2: Protein | Mass: 87873.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP1, CHLREDRAFT_196412 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27YU0 |
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#4: Protein | Mass: 77445.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP2, CHLREDRAFT_186281 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6UBQ3 |
#6: Protein | Mass: 39361.293 Da / Num. of mol.: 1 / Fragment: UNP residues 159-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12759 |
#7: Protein | Mass: 55928.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP5, CHLREDRAFT_190792 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27YU7, Oxidoreductases |
#9: Protein | Mass: 49900.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01656 |
#10: Protein | Mass: 48884.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01657 |
#11: Protein/peptide | Mass: 528.644 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm) |
#12: Protein/peptide | Mass: 443.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm) |
#13: Protein | Mass: 7592.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm) |
#14: Protein | Mass: 5890.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm) |
-Protein / Protein/peptide , 2 types, 2 molecules KJ
#3: Protein | Mass: 61422.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RSP23, CHLRE_16g654300v5, CHLREDRAFT_139197 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q69B19, nucleoside-diphosphate kinase |
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#5: Protein/peptide | Mass: 358.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chlamydomonas reinhardtii radial spoke head and neck / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 / Details: 30 mM HEPES, 300 mM NaCl, 1 mM TCEP |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7572 |
Image scans | Movie frames/image: 35 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 942591 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136659 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7JR9 |