[English] 日本語
Yorodumi
- PDB-7jtk: Radial spoke 1 isolated from Chlamydomonas reinhardtii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jtk
TitleRadial spoke 1 isolated from Chlamydomonas reinhardtii
Components
  • (Flagellar radial spoke protein ...) x 14
  • Cytochrome b5 heme-binding domain-containing protein
  • Dynein 8 kDa light chain, flagellar outer arm
  • Predicted proteinProtein structure prediction
  • Uncharacterized protein
  • Unknown protein
KeywordsSTRUCTURAL PROTEIN / cilia / native / complex / mechanoregulation
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 / Set1C/COMPASS 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 / Set1C/COMPASS complex / UTP biosynthetic process / ciliary plasm / CTP biosynthetic process / Oxidoreductases / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / axoneme / chaperone cofactor-dependent protein refolding / cilium assembly / microtubule-based process / protein peptidyl-prolyl isomerization / centriole / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cilium / unfolded protein binding / protein folding / mitotic cell cycle / protein-folding chaperone binding / microtubule / oxidoreductase activity / cytoskeleton / calmodulin binding / phosphorylation / calcium ion binding / ATP binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase 6 / Radial spoke protein 14 / IQ and ubiquitin-like domain-containing protein / Radial spokehead-like protein / Radial spoke 3 / Radial spokehead-like protein / Radial spoke protein 3 / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif ...Nucleoside diphosphate kinase 6 / Radial spoke protein 14 / IQ and ubiquitin-like domain-containing protein / Radial spokehead-like protein / Radial spoke 3 / Radial spokehead-like protein / Radial spoke protein 3 / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / MORN motif / HSP40/DnaJ peptide-binding / MORN repeat / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / EF hand / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / DnaJ domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / IQ calmodulin-binding motif / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / EF-hand domain pair / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Armadillo/plakoglobin ARM repeat profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Armadillo/beta-catenin-like repeats / Armadillo / IQ motif profile. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / IQ motif, EF-hand binding site / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Armadillo-like helical / EF-hand domain pair / Armadillo-type fold
Similarity search - Domain/homology
PHOSPHATE ION / IQ and ubiquitin-like domain-containing protein / Cytochrome b5 heme-binding domain-containing protein / EF-hand domain-containing protein / Radial spoke protein 14 / Peptidyl-prolyl cis-trans isomerase / Radial spoke protein 4 / Radial spoke protein 16 / Uncharacterized protein / Predicted protein ...PHOSPHATE ION / IQ and ubiquitin-like domain-containing protein / Cytochrome b5 heme-binding domain-containing protein / EF-hand domain-containing protein / Radial spoke protein 14 / Peptidyl-prolyl cis-trans isomerase / Radial spoke protein 4 / Radial spoke protein 16 / Uncharacterized protein / Predicted protein / Flagellar radial spoke protein 3 / Flagellar radial spoke protein 4 / Flagellar radial spoke protein 6 / Flagellar radial spoke protein 1 / Radial spoke protein 11 / Radial spoke protein 10 / Radial spoke head protein 9 homolog / Flagellar radial spoke protein 5 / Dynein 8 kDa light chain, flagellar outer arm / Nucleoside diphosphate kinase 6 / Flagellar radial spoke protein 2
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGui, 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, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: 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
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-22475
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22475
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar radial spoke protein 1
B: Flagellar radial spoke protein 1
C: Flagellar radial spoke protein 2
D: Flagellar radial spoke protein 2
E: Flagellar radial spoke protein 3
F: Flagellar radial spoke protein 3
G: Flagellar radial spoke protein 4
H: Flagellar radial spoke protein 4
I: Flagellar radial spoke protein 5
J: Flagellar radial spoke protein 5
K: Flagellar radial spoke protein 6
L: Flagellar radial spoke protein 6
M: Flagellar radial spoke protein 7
N: Flagellar radial spoke protein 7
O: Flagellar radial spoke protein 9
P: Flagellar radial spoke protein 9
Q: Flagellar radial spoke protein 9
R: Flagellar radial spoke protein 9
S: Flagellar radial spoke protein 10
T: Flagellar radial spoke protein 10
U: Flagellar radial spoke protein 11
V: Flagellar radial spoke protein 11
W: Flagellar radial spoke protein 12
X: Flagellar radial spoke protein 14
Y: Flagellar radial spoke protein 16
Z: Flagellar radial spoke protein 16
a: Dynein 8 kDa light chain, flagellar outer arm
b: Dynein 8 kDa light chain, flagellar outer arm
c: Dynein 8 kDa light chain, flagellar outer arm
d: Dynein 8 kDa light chain, flagellar outer arm
e: Unknown protein
i: Flagellar radial spoke protein 23
j: Flagellar radial spoke protein 23
k: Cytochrome b5 heme-binding domain-containing protein
s: Uncharacterized protein
u: Predicted protein
v: Predicted protein
y: Flagellar radial spoke protein 16
z: Flagellar radial spoke protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,572,37843
Polymers1,571,99839
Non-polymers3804
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Flagellar radial spoke protein ... , 14 types, 30 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZyzij

#1: Protein Flagellar radial spoke protein 1


Mass: 87873.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU0
#2: Protein Flagellar radial spoke protein 2


Mass: 77445.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UBQ3
#3: Protein Flagellar radial spoke protein 3


Mass: 56856.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J2J7, UniProt: P12759*PLUS
#4: Protein Flagellar radial spoke protein 4


Mass: 49843.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I550, UniProt: Q01656*PLUS
#5: Protein Flagellar radial spoke protein 5


Mass: 55403.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU7, Oxidoreductases
#6: Protein Flagellar radial spoke protein 6


Mass: 48884.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q01657
#7: Protein Flagellar radial spoke protein 7


Mass: 54781.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DL29
#8: Protein
Flagellar radial spoke protein 9


Mass: 29572.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU5
#9: Protein Flagellar radial spoke protein 10


Mass: 23553.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU4
#10: Protein Flagellar radial spoke protein 11


Mass: 21504.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU3
#11: Protein Flagellar radial spoke protein 12 / PPIase


Mass: 19632.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I2U9, peptidylprolyl isomerase
#12: Protein Flagellar radial spoke protein 14 / Flagellar-associated protein 132


Mass: 40597.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNV0
#13: Protein
Flagellar radial spoke protein 16


Mass: 39052.676 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IKR9
#16: Protein Flagellar radial spoke protein 23 / radial spoke protein 23


Mass: 61422.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q69B19, nucleoside-diphosphate kinase

-
Protein , 4 types, 8 molecules abcdksuv

#14: Protein
Dynein 8 kDa light chain, flagellar outer arm


Mass: 10336.775 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39580
#17: Protein Cytochrome b5 heme-binding domain-containing protein


Mass: 26609.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DCN8
#18: Protein Uncharacterized protein


Mass: 75037.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D359
#19: Protein Predicted protein / Protein structure prediction


Mass: 8111.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JDM3

-
Protein/peptide / Non-polymers , 2 types, 5 molecules e

#15: Protein/peptide Unknown protein


Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#20: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: radial spoke 1 / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-1690 / Organelle: cilia
Buffer solutionpH: 7.4
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2RELIONparticle selection
3SerialEMimage acquisition
5CTFFINDCTF correction
6RELIONCTF correction
9UCSF Chimeramodel fitting
10Cootmodel fitting
15RELION3.13D reconstruction
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2320543
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 221836 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more