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- EMDB-22480: Cryo-EM density map of stalk of radial spoke 1 attached with doub... -

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Basic information

Entry
Database: EMDB / ID: EMD-22480
TitleCryo-EM density map of stalk of radial spoke 1 attached with doublet microtubule from Chlamydomonas reinhardtii
Map data
Sample
  • Complex: stalk of radial spoke 1
    • Protein or peptide: Radial spoke protein 3
    • Protein or peptide: Dynein 8 kDa light chain, flagellar outer arm
    • Protein or peptide: FAP207
    • Protein or peptide: FAP253
    • Protein or peptide: Calmodulin
Keywordscilia / 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 / ciliary plasm / motile cilium / axoneme / enzyme regulator activity / microtubule-based process / acrosomal vesicle ...radial spoke / positive regulation of cilium-dependent cell motility / motile cilium assembly / dynein complex / ciliary plasm / motile cilium / axoneme / enzyme regulator activity / microtubule-based process / acrosomal vesicle / calcium-mediated signaling / cilium / microtubule / cytoskeleton / calcium ion binding / membrane / cytoplasm
Similarity search - Function
IQ and ubiquitin-like domain-containing protein / Radial spoke 3 / Calmodulin / 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. / MORN motif / MORN repeat / Dynein light chain type 1 ...IQ and ubiquitin-like domain-containing protein / Radial spoke 3 / Calmodulin / 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. / MORN motif / MORN repeat / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / IQ motif profile. / 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 / EF-hand domain pair
Similarity search - Domain/homology
IQ and ubiquitin-like domain-containing protein / MORN repeat-containing protein 3 / Calmodulin / Uncharacterized protein / Calmodulin / Flagellar radial spoke protein 3 / Dynein 8 kDa light chain, flagellar outer arm
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 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, 1 items
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 18, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jts
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jts
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22480.png

Downloads & links

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Map

FileDownload / File: emd_22480.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.403 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.019428184 - 0.049267717
Average (Standard dev.)0.00000423531 (±0.00027315933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions832832832
Spacing832832832
CellA=B=C: 1167.296 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4031.4031.403
M x/y/z832832832
origin x/y/z0.0000.0000.000
length x/y/z1167.2961167.2961167.296
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS832832832
D min/max/mean-0.0190.0490.000

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Supplemental data

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Mask #1

Fileemd_22480_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : stalk of radial spoke 1

EntireName: stalk of radial spoke 1
Components
  • Complex: stalk of radial spoke 1
    • Protein or peptide: Radial spoke protein 3
    • Protein or peptide: Dynein 8 kDa light chain, flagellar outer arm
    • Protein or peptide: FAP207
    • Protein or peptide: FAP253
    • Protein or peptide: Calmodulin

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Supramolecule #1: stalk of radial spoke 1

SupramoleculeName: stalk of radial spoke 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-125 / Organelle: cilia

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Macromolecule #1: Radial spoke protein 3

MacromoleculeName: Radial spoke protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 56.856688 KDa
SequenceString: 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

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Macromolecule #2: Dynein 8 kDa light chain, flagellar outer arm

MacromoleculeName: Dynein 8 kDa light chain, flagellar outer arm / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 10.336775 KDa
SequenceString:
MASGSSKAVI KNADMSEEMQ ADAVDCATQA LEKYNIEKDI AAYIKKEFDR KHNPTWHCIV GRNFGSYVTH ETKHFIYFYL GQVAILLFK SG

UniProtKB: Dynein 8 kDa light chain, flagellar outer arm

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Macromolecule #3: FAP207

MacromoleculeName: FAP207 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.41841 KDa
SequenceString: 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

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Macromolecule #4: FAP253

MacromoleculeName: FAP253 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 75.037945 KDa
SequenceString: 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

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Macromolecule #5: Calmodulin

MacromoleculeName: Calmodulin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 18.317215 KDa
SequenceString:
MAANTEQLTE EQIAEFKEAF ALFDKDGDGT ITTKELGTVM RSLGQNPTEA ELQDMISEVD ADGNGTIDFP EFLMLMARKM KETDHEDEL REAFKVFDKD GNGFISAAEL RHVMTNLGEK LSEEEVDEMI READVDGDGQ VNYEEFVRMM TSGATDDKDK K GHK

UniProtKB: Calmodulin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE
DetailsThis sample is attached with doublet microtubule

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial model was extracted from a doublet microtubule attached density in our dataset.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied 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

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7jts:
Stalk of radial spoke 1 attached with doublet microtubule from Chlamydomonas reinhardtii

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