+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8539 | |||||||||
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Title | Cryo-EM map of protofilament of microtubule doublet | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information structural constituent of cytoskeleton / microtubule cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Ichikawa M / Liu D / Kastritis PL / Basu K / Bui KH | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nat Commun / Year: 2017 Title: Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins. Authors: Muneyoshi Ichikawa / Dinan Liu / Panagiotis L Kastritis / Kaustuv Basu / Tzu Chin Hsu / Shunkai Yang / Khanh Huy Bui / Abstract: Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the ...Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule. | |||||||||
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_8539.map.gz | 2.4 MB | EMDB map data format | |
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Header (meta data) | emd-8539-v30.xml emd-8539.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_8539.png | 108.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8539 | HTTPS FTP |
-Validation report
Summary document | emd_8539_validation.pdf.gz | 338.6 KB | Display | EMDB validaton report |
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Full document | emd_8539_full_validation.pdf.gz | 338.1 KB | Display | |
Data in XML | emd_8539_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_8539_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8539 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8539 | HTTPS FTP |
-Related structure data
Related structure data | 5ucyMC 8528C 8532C 8537C 5ubqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8539.map.gz / Format: CCP4 / Size: 27.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.375 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 : Protofilament from ciliary microtubule doublet
Entire | Name: Protofilament from ciliary microtubule doublet |
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Components |
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-Supramolecule #1: Protofilament from ciliary microtubule doublet
Supramolecule | Name: Protofilament from ciliary microtubule doublet / 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 |
-Macromolecule #1: Tubulin alpha chain
Macromolecule | Name: Tubulin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 48.788254 KDa |
Sequence | String: MREVISIHVG QGGIQVGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRAVFLDL EPTVIDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLCL DRIRKLADNC TGLQGFLVFN SVGGGTGSGL GSLLLERLSV D YGKKSKLG ...String: MREVISIHVG QGGIQVGNAC WELFCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRAVFLDL EPTVIDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLCL DRIRKLADNC TGLQGFLVFN SVGGGTGSGL GSLLLERLSV D YGKKSKLG FTIYPSPQVS TAVVEPYNSI LSTHSLLEHT DVAVMLDNEA IYDICRRNLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDITEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNSAFE PANMMAKCDP RHGKYMACSM MYR GDVVPK DVNASIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVMRAVC MISNSTAIAE VFSRLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDYEEV GIETAE |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 48.009199 KDa |
Sequence | String: MREIVHIQGG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGRYV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS ...String: MREIVHIQGG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGRYV PRAILMDLEP GTMDSVRAGP FGQLFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAEGCDC LQGFQITHSL GGGTGSGMGT LLISKVREEY P DRIMETFS VVPSPKVSDT VVEPYNATLS VHQLVENADE CMVIDNEALY DICFRTLKLT TPTYGDLNHL VSAAMSGVTC CL RFPGQLN SDLRKLAVNL IPFPRLHFFM IGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMCAADPRH GRYLTASALF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNIKSSICDI PPKGLKMAVT FVGNSTAIQE MFKRVAEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDAT |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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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 - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 4 / Number real images: 5983 / 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: 50.0 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: BACKBONE TRACE / Target criteria: minimization global |
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Output model | PDB-5ucy: |