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Yorodumi- EMDB-20606: Cryo-EM map of the A-tubule prepared by 0.2% Sarkosyl treatment -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20606 | ||||||||||||
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Title | Cryo-EM map of the A-tubule prepared by 0.2% Sarkosyl treatment | ||||||||||||
Map data | Cryo-EM map of the A-tubule prepared by 0.2% Sarkosyl treatment | ||||||||||||
Sample |
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Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||
Authors | Ichikawa M / Khalifa AAZ / Vargas J / Basu K / Bui KH | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Authors: Muneyoshi Ichikawa / Ahmad Abdelzaher Zaki Khalifa / Shintaroh Kubo / Daniel Dai / Kaustuv Basu / Mohammad Amin Faghfor Maghrebi / Javier Vargas / Khanh Huy Bui / Abstract: Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic ...Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a-tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20606.map.gz | 33.4 MB | EMDB map data format | |
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Header (meta data) | emd-20606-v30.xml emd-20606.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20606_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_20606.png | 130.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20606 | HTTPS FTP |
-Validation report
Summary document | emd_20606_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_20606_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_20606_validation.xml.gz | 496 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20606 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20606 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20606.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the A-tubule prepared by 0.2% Sarkosyl treatment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.751 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 48nm-repeat of A-tubule from the doublet microtubule
Entire | Name: 48nm-repeat of A-tubule from the doublet microtubule |
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Components |
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-Supramolecule #1: 48nm-repeat of A-tubule from the doublet microtubule
Supramolecule | Name: 48nm-repeat of A-tubule from the doublet microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Organelle: cilia / Location in cell: cilia |
-Supramolecule #2: Tubulin lattice
Supramolecule | Name: Tubulin lattice / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Organelle: cilia / Location in cell: cilia |
-Supramolecule #3: Microtubule Inner Proteins
Supramolecule | Name: Microtubule Inner Proteins / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: SB255 / Organelle: cilia / Location in cell: cilia |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 3 for 5 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number real images: 5179 / Average exposure time: 1.4 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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