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- EMDB-20855: 48-nm repeat unit of the doublet microtubule from Chlamydomonas r... -

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Basic information

Entry
Database: EMDB / ID: EMD-20855
Title48-nm repeat unit of the doublet microtubule from Chlamydomonas reinhardtii
Map data48nm repeat of the Chlamydomonas doublet microtubule
Sample
  • Organelle or cellular component: 48nm-repeat of doublet microtubule
    • Complex: Tubulin lattice
Function / homology
Function and homology information


axonemal central pair / axonemal outer doublet / membrane-bounded organelle / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / axoneme assembly / axonemal microtubule / intracellular organelle / motile cilium ...axonemal central pair / axonemal outer doublet / membrane-bounded organelle / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / axoneme assembly / axonemal microtubule / intracellular organelle / motile cilium / microtubule associated complex / cilium assembly / microtubule-based process / Hsp70 protein binding / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / structural constituent of cytoskeleton / microtubule / cytoskeleton / calmodulin binding / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Protein Flattop / Enkurin domain / Calmodulin-binding / Enkurin domain profile. / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / Tubulin-beta mRNA autoregulation signal. ...Protein Flattop / Enkurin domain / Calmodulin-binding / Enkurin domain profile. / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / 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 / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cilia- and flagella-associated protein 52 / Flagellar associated protein / Cilia- and flagella-associated protein 20 / Protein Flattop homolog / Uncharacterized protein / Parkin-co-regulated gene product / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.57 Å
AuthorsKhalifa AAZ / Ichikawa M / Bui KH
Funding support Canada, 3 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (Canada)RGPIN-2016-04954 Canada
Natural Sciences and Engineering Research Council (Canada)RGPIN-2018-04813 Canada
Canadian Institutes of Health ResearchPJT-156354 Canada
CitationJournal: Elife / Year: 2020
Title: The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications.
Authors: Ahmad Abdelzaher Zaki Khalifa / Muneyoshi Ichikawa / Daniel Dai / Shintaroh Kubo / Corbin Steven Black / Katya Peri / Thomas S McAlear / Simon Veyron / Shun Kai Yang / Javier Vargas / ...Authors: Ahmad Abdelzaher Zaki Khalifa / Muneyoshi Ichikawa / Daniel Dai / Shintaroh Kubo / Corbin Steven Black / Katya Peri / Thomas S McAlear / Simon Veyron / Shun Kai Yang / Javier Vargas / Susanne Bechstedt / Jean-François Trempe / Khanh Huy Bui /
Abstract: Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate ...Microtubules are cytoskeletal structures involved in stability, transport and organization in the cell. The building blocks, the α- and β-tubulin heterodimers, form protofilaments that associate laterally into the hollow microtubule. Microtubule also exists as highly stable doublet microtubules in the cilia where stability is needed for ciliary beating and function. The doublet microtubule maintains its stability through interactions at its inner and outer junctions where its A- and B-tubules meet. Here, using cryo-electron microscopy, bioinformatics and mass spectrometry of the doublets of and , we identified two new inner junction proteins, FAP276 and FAP106, and an inner junction-associated protein, FAP126, thus presenting the complete answer to the inner junction identity and localization. Our structural study of the doublets shows that the inner junction serves as an interaction hub that involves tubulin post-translational modifications. These interactions contribute to the stability of the doublet and hence, normal ciliary motility.
History
DepositionOct 21, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseJan 29, 2020-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ve7
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ve7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20855.png

Downloads & links

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Map

FileDownload / File: emd_20855.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation48nm repeat of the Chlamydomonas doublet microtubule
Voxel sizeX=Y=Z: 1.751 Å
Density
Contour LevelBy AUTHOR: 14 / Movie #1: 14
Minimum - Maximum-37.361267 - 62.641747
Average (Standard dev.)0.3395614 (±5.0451717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions402402402
Spacing402402402
CellA=B=C: 703.90204 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7511.7511.751
M x/y/z402402402
origin x/y/z0.0000.0000.000
length x/y/z703.902703.902703.902
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS402402402
D min/max/mean-37.36162.6420.340

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Supplemental data

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Sample components

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Entire : 48nm-repeat of doublet microtubule

EntireName: 48nm-repeat of doublet microtubule
Components
  • Organelle or cellular component: 48nm-repeat of doublet microtubule
    • Complex: Tubulin lattice

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Supramolecule #1: 48nm-repeat of doublet microtubule

SupramoleculeName: 48nm-repeat of doublet microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: cc124 / Organelle: cilia / Location in cell: cilia

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Supramolecule #2: Tubulin lattice

SupramoleculeName: Tubulin lattice / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC124 / Organelle: cilia / Location in cell: cilia

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 3 for 5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number real images: 9528 / Average exposure time: 1.4 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 122997
CTF correctionSoftware - Name: RELION (ver. 3.0)
Startup modelType of model: EMDB MAP
EMDB ID:

8537

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER (ver. 19.02) / Details: Hel
Final 3D classificationNumber classes: 3 / Software - Name: FREALIGN (ver. 9.03)
Final angle assignmentType: PROJECTION MATCHING / Software: (Name: RELION (ver. 3.0), FREALIGN (ver. 9.03))
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 122997
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 190
Output model

PDB-6ve7:
The inner junction complex of Chlamydomonas reinhardtii doublet microtubule

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