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- PDB-7ju4: Radial spoke 2 stalk, IDAc, and N-DRC attached with doublet micro... -

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Entry
Database: PDB / ID: 7ju4
TitleRadial spoke 2 stalk, IDAc, and N-DRC attached with doublet microtubule
Components
  • (Dynein regulatory complex subunit ...) x 2
  • (Flagellar-associated protein ...) x 2
  • (Radial spoke protein ...) x 4
  • 28 kDa inner dynein arm light chain, axonemal
  • Actin
  • CFAP91 domain-containing protein
  • Dynein 8 kDa light chain, flagellar outer arm
  • Dynein regulatory complex protein 1
  • FAP207
  • FAP253
  • Radial spike protein 8
  • Tubulin alpha
  • Tubulin beta
  • Unknown protein
KeywordsSTRUCTURAL PROTEIN / cilia / native / complex / microtubule / mechanoregulation
Function / homology
Function and homology information


inner dynein arm / regulation of cilium movement / axonemal dynein complex assembly / axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement / dynein heavy chain binding ...inner dynein arm / regulation of cilium movement / axonemal dynein complex assembly / axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement / dynein heavy chain binding / axoneme assembly / motile cilium assembly / dynein complex / ciliary plasm / motile cilium / axoneme / microtubule-based process / centriole / GTPase activator activity / acrosomal vesicle / cell projection / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cilium / structural constituent of cytoskeleton / small GTPase binding / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP binding / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Axonemal dynein light chain / Dynein regulatory complex protein 1, C-terminal / Axonemal dynein light chain / Sperm tail C-terminal domain / Radial spoke protein 14 / : / Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 ...Axonemal dynein light chain / Dynein regulatory complex protein 1, C-terminal / Axonemal dynein light chain / Sperm tail C-terminal domain / Radial spoke protein 14 / : / Cilia- and flagella-associated protein 91 / CFAP91 domain / Coiled-coil domain-containing protein 39 / Coiled-coil domain-containing protein 40 / Cilia- and flagella-associated protein 91 / IQ and ubiquitin-like domain-containing protein / Growth arrest-specific protein 8 domain / Growth arrest-specific protein 8 / Dynein regulatory complex protein 1/2, N-terminal / Dynein regulatory complex protein / Growth-arrest specific micro-tubule binding / Sperm tail / Radial spoke 3 / Radial spoke protein 3 / : / : / 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 / MORN repeat / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / EF hand / Leucine rich repeat, ribonuclease inhibitor type / IQ calmodulin-binding motif / Leucine Rich repeat / EF-hand domain pair / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Actin / Actin family / Actin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Leucine-rich repeat / EF-hand domain pair / Leucine-rich repeat domain superfamily / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / 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
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Flagellar-associated protein 172 / Flagellar-associated protein 59 / IQ and ubiquitin-like domain-containing protein / Flagellar associated protein / MORN repeat-containing protein 3 / Cilia- and flagella-associated protein 91 / EF-hand domain-containing protein ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Flagellar-associated protein 172 / Flagellar-associated protein 59 / IQ and ubiquitin-like domain-containing protein / Flagellar associated protein / MORN repeat-containing protein 3 / Cilia- and flagella-associated protein 91 / EF-hand domain-containing protein / Uncharacterized protein / Dynein regulatory complex subunit 2 / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Dynein regulatory complex protein 1 / Actin / Radial spoke protein 11 / Radial spike protein 8 / Dynein 8 kDa light chain, flagellar outer arm / 28 kDa inner dynein arm light chain, axonemal / Dynein regulatory complex subunit 4
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 19, 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
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
0: Dynein regulatory complex subunit 4
1: Dynein regulatory complex protein 1
2: Dynein regulatory complex subunit 2
3: Unknown protein
4: Dynein regulatory complex subunit 4
6: Tubulin beta
7: Tubulin alpha
8: Tubulin beta
9: Tubulin alpha
A: Flagellar-associated protein 59
B: Flagellar-associated protein 172
C: Tubulin beta
D: Tubulin alpha
E: Radial spoke protein 3
F: Radial spoke protein 3
G: Tubulin beta
H: Tubulin alpha
I: Tubulin beta
J: Tubulin alpha
K: Tubulin beta
L: Tubulin alpha
M: Radial spoke protein 7
N: Radial spoke protein 7
O: Tubulin beta
P: Tubulin alpha
Q: Tubulin beta
R: Tubulin alpha
S: Tubulin beta
T: Tubulin alpha
U: Radial spoke protein 11
V: Radial spoke protein 11
W: Tubulin beta
X: Tubulin alpha
Y: Tubulin beta
Z: Tubulin alpha
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: Dynein 8 kDa light chain, flagellar outer arm
f: Dynein 8 kDa light chain, flagellar outer arm
g: Dynein 8 kDa light chain, flagellar outer arm
h: Dynein 8 kDa light chain, flagellar outer arm
i: Tubulin beta
j: Tubulin alpha
k: Tubulin beta
l: Radial spoke protein 15
m: FAP207
n: Radial spike protein 8
o: Dynein 8 kDa light chain, flagellar outer arm
p: Dynein 8 kDa light chain, flagellar outer arm
q: Dynein 8 kDa light chain, flagellar outer arm
r: Dynein 8 kDa light chain, flagellar outer arm
s: FAP253
t: Tubulin alpha
u: Actin
v: 28 kDa inner dynein arm light chain, axonemal
w: 28 kDa inner dynein arm light chain, axonemal
x: CFAP91 domain-containing protein
y: Tubulin beta
z: Tubulin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,675,852104
Polymers2,661,47561
Non-polymers14,37743
Water00
1


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

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Components

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Dynein regulatory complex subunit ... , 2 types, 3 molecules 042

#1: Protein Dynein regulatory complex subunit 4 / Growth arrest-specific protein 8 homolog / Protein PF2


Mass: 55207.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7XJ96
#3: Protein Dynein regulatory complex subunit 2 / Coiled-coil domain-containing protein 65 homolog / Flagellar-associated protein 250


Mass: 64986.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JB22

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Protein , 11 types, 49 molecules 1368CGIKOQSWYiky79DHJLPRTXZjtz...

#2: Protein Dynein regulatory complex protein 1


Mass: 79454.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P0DL09
#4: Protein Unknown protein


Mass: 6145.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#5: Protein
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#6: Protein
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204
#12: Protein
Dynein 8 kDa light chain, flagellar outer arm


Mass: 10336.775 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39580
#14: Protein FAP207


Mass: 28418.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DJP7
#15: Protein Radial spike protein 8 / Radial spoke protein 8


Mass: 40537.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q27YU6
#16: Protein FAP253


Mass: 75037.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D359
#17: Protein Actin


Mass: 41881.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P53498
#18: Protein 28 kDa inner dynein arm light chain, axonemal / p28


Mass: 28691.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39604
#19: Protein CFAP91 domain-containing protein / FAP91


Mass: 134440.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DJU2

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Flagellar-associated protein ... , 2 types, 2 molecules AB

#7: Protein Flagellar-associated protein 59 / CCDC39


Mass: 105504.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A0A1H1F6
#8: Protein Flagellar-associated protein 172 / CCDC40


Mass: 101385.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A0A1GYE8

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Radial spoke protein ... , 4 types, 7 molecules EFMNUVl

#9: Protein 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
#10: Protein 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
#11: Protein 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
#13: Protein Radial spoke protein 15


Mass: 35302.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DEQ5

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Non-polymers , 4 types, 43 molecules

#20: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#21: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#22: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#23: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of radial spoke 2 stalk, IDAc, and N-DRC attached with doublet microtubule
Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingAverage exposure time: 9 sec. / Electron dose: 38.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
5RELION3.1CTF correction
8UCSF Chimeramodel fitting
9Cootmodel fitting
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202168 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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