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Yorodumi- EMDB-20858: The inner junction complex of Chlamydomonas reinhardtii doublet m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20858 | ||||||||||||
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Title | The inner junction complex of Chlamydomonas reinhardtii doublet microtubule | ||||||||||||
Map data | 16-nm repeating unit of Chlamydomonas inner junction | ||||||||||||
Sample |
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Function / homology | Function and homology information axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / membrane-bounded organelle / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / axoneme assembly / axonemal microtubule / cilium organization / motile cilium ...axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / membrane-bounded organelle / regulation of cilium beat frequency involved in ciliary motility / establishment of protein localization to organelle / axoneme assembly / axonemal microtubule / cilium organization / motile cilium / microtubule associated complex / intracellular non-membrane-bounded organelle / axoneme / microtubule-based process / cilium assembly / Hsp70 protein binding / ciliary basal body / Hsp90 protein binding / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / calmodulin binding / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Khalifa AAZ / Ichikawa M / Bui KH | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: 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 |
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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_20858.map.gz | 100 MB | EMDB map data format | |
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Header (meta data) | emd-20858-v30.xml emd-20858.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20858_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_20858.png | 146.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20858 | HTTPS FTP |
-Validation report
Summary document | emd_20858_validation.pdf.gz | 529.6 KB | Display | EMDB validaton report |
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Full document | emd_20858_full_validation.pdf.gz | 529.2 KB | Display | |
Data in XML | emd_20858_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_20858_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20858 | HTTPS FTP |
-Related structure data
Related structure data | 6ve7MC 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_20858.map.gz / Format: CCP4 / Size: 108.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 16-nm repeating unit of Chlamydomonas inner junction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.875 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 : Inner junction complex of the cilia
Entire | Name: Inner junction complex of the cilia |
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Components |
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-Supramolecule #1: Inner junction complex of the cilia
Supramolecule | Name: Inner junction complex of the cilia / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: CC124 / Organelle: cilia |
Molecular weight | Experimental: 1 MDa |
-Macromolecule #1: Tubulin beta
Macromolecule | Name: Tubulin beta / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 49.665809 KDa |
Sequence | String: MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS ...String: MREIVHIQGG QCGNQIGAKF WEVVSDEHGI DPTGTYHGDS DLQLERINVY FNEATGGRYV PRAILMDLEP GTMDSVRSGP YGQIFRPDN FVFGQTGAGN NWAKGHYTEG AELIDSVLDV VRKEAESCDC LQGFQVCHSL GGGTGSGMGT LLISKIREEY P DRMMLTFS VVPSPKVSDT VVEPYNATLS VHQLVENADE CMVLDNEALY DICFRTLKLT TPTFGDLNHL ISAVMSGITC CL RFPGQLN ADLRKLAVNL IPFPRLHFFM VGFTPLTSRG SQQYRALTVP ELTQQMWDAK NMMCAADPRH GRYLTASALF RGR MSTKEV DEQMLNVQNK NSSYFVEWIP NNVKSSVCDI PPKGLKMSAT FIGNSTAIQE MFKRVSEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDASAEEEGE FEGEEEEA |
-Macromolecule #2: Flagellar associated protein
Macromolecule | Name: Flagellar associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 27.019803 KDa |
Sequence | String: MQEESVYALI PQPQEVPQRP AMHTSKFGGK THPAQFDFGQ NKVQPHATMG RPDGANGPAF LHAHEKEPKL PSPGPPSNPK QKIRPPVPA KEEKPTMGLT SNKNFITANA VDVILAKPGK VPQPEFQWTQ KPDYGKVPMY LKRNKDRVAK EKEHFTQYLR M REAPEANA ...String: MQEESVYALI PQPQEVPQRP AMHTSKFGGK THPAQFDFGQ NKVQPHATMG RPDGANGPAF LHAHEKEPKL PSPGPPSNPK QKIRPPVPA KEEKPTMGLT SNKNFITANA VDVILAKPGK VPQPEFQWTQ KPDYGKVPMY LKRNKDRVAK EKEHFTQYLR M REAPEANA HVSQLSPEDR QQLVRHLKAK WGSVNTAYQG LSLSVDSAVK KGRKEAMERE LAEIERDIRT LERGEVVLVV DD |
-Macromolecule #3: Tubulin alpha
Macromolecule | Name: Tubulin alpha / type: protein_or_peptide / ID: 3 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 49.638008 KDa |
Sequence | String: MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG ...String: MREVISIHIG QAGIQVGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDAFN TFFSETGAGK HVPRCIFLDL EPTVVDEVRT GTYRQLFHP EQLISGKEDA ANNFARGHYT IGKEIVDLAL DRIRKLADNC TGLQGFLVFN AVGGGTGSGL GSLLLERLSV D YGKKSKLG FTVYPSPQVS TAVVEPYNSV LSTHSLLEHT DVAVMLDNEA IYDICRRSLD IERPTYTNLN RLIAQVISSL TA SLRFDGA LNVDITEFQT NLVPYPRIHF MLSSYAPIIS AEKAYHEQLS VAEITNAAFE PASMMVKCDP RHGKYMACCL MYR GDVVPK DVNASVATIK TKRTIQFVDW CPTGFKCGIN YQPPTVVPGG DLAKVQRAVC MISNSTAIGE IFSRLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDL AALEKDFEEV GAESAEGAGE GEGEEY |
-Macromolecule #4: FAP276
Macromolecule | Name: FAP276 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 10.073385 KDa |
Sequence | String: MDLKQQVKNY TMTIRNTRPP TMIKEQDKSE FSHFRALQVL ANGDEVPYEA TLRNVIHDGA RQPKLPPRQT QKHPGYIRNE SGGFFTS |
-Macromolecule #5: Protein Flattop homolog
Macromolecule | Name: Protein Flattop homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 15.435397 KDa |
Sequence | String: MSRSYPGEQV EHAFNSKRLK NWEVPAVDKS QAISTSTGTR FGTLQPRSGR TQFIVDDNGH LKSGVPKLEK SAFNFTQTTP VFMDSAPRW PKENPTWPKN MKATMGYKGI QSNYLPTNTV TLKAVEVPGT TERNFNFM |
-Macromolecule #6: Cilia- and flagella-associated protein 20
Macromolecule | Name: Cilia- and flagella-associated protein 20 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 22.193566 KDa |
Sequence | String: MFKNAFQSGF LSVLYSIGSK PLEIWDKQVS NGHIKRITDA DIQSSVLEIM GQNVSTTYIT CPADPNKTLG IKLPFLVLII KNLNKYFSF EVQVLDDKNV RRRFRASNYQ STTRVKPFIC TMPMRLDSGW NQIQFNLSDF TRRAYGTNYI ETLRVQVHAN C RIRRIYFS DRLYSEEELP AEFKLFLPIQ KS |
-Macromolecule #7: PACRG
Macromolecule | Name: PACRG / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 34.215148 KDa |
Sequence | String: MNGDVAGSLF TSTYRNVKLA GKAPPAANLS GTGSCFDTTS LSPARAGAHK ALDVQKDELP VWSKSTLSYK YPAGRPNPTG FLKKGDGEM IKTKTGGFEE RKPSPPQAGA YKRRENPPNT AFRRFYERGD LPIAVDHRGS KNMIAWKVDI EKLDYHHYLP I FFDGIRET ...String: MNGDVAGSLF TSTYRNVKLA GKAPPAANLS GTGSCFDTTS LSPARAGAHK ALDVQKDELP VWSKSTLSYK YPAGRPNPTG FLKKGDGEM IKTKTGGFEE RKPSPPQAGA YKRRENPPNT AFRRFYERGD LPIAVDHRGS KNMIAWKVDI EKLDYHHYLP I FFDGIRET QEPYRFLAVK GVEDMLRVGG SKILPVIPQL IIPIKTALNT RDHSVMCITL QLLQKLVLSA DLVGEALVPY YR QILPIFN LYKNKNKNLG DGIDYGQRNY DCLGELIADT LALFEQKGGD DAFINIKYMV PTYESSVNYA |
-Macromolecule #8: FAP52
Macromolecule | Name: FAP52 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
Molecular weight | Theoretical: 68.546508 KDa |
Sequence | String: MAEPLVLNSV IGFGGAIENG LIAHPDGRTI IYPLGSTIVL RDRADPRSQE FLQGHSDKVS CLALSRSGRY LASGQITYMG FTADIIIWD LESKQLIHRM ALHKVKVQAL DFSCDERFLA SLGGQDDNAL VLWDVASGNA ICGSPCNTNF TNCVKFFNNS P DKLITAGN ...String: MAEPLVLNSV IGFGGAIENG LIAHPDGRTI IYPLGSTIVL RDRADPRSQE FLQGHSDKVS CLALSRSGRY LASGQITYMG FTADIIIWD LESKQLIHRM ALHKVKVQAL DFSCDERFLA SLGGQDDNAL VLWDVASGNA ICGSPCNTNF TNCVKFFNNS P DKLITAGN FNMNVWTYDA GNNKLRPTDA TLGTLKRVFK SVVVDANDEY AYCGTTTGDV LQIALERVLF KNTGPAKGNV QM GVTATCE VPTGDILVGG GDGSLQVLRT VPEPSSTNPK LLRKMPALAG TKVEGAITSI ALADMNARGF TFFVGTAMCN IYK VTYEPA TSRLKEELVQ TAHNDKINGM AFPNEYSEVF ATCGTGFIRL WHLTTCRELL RIAVPNLECF CIAFTTDGSA ILSG WSDGK IRAFGPQSGK IIFTINDAHQ KAVTAIASTA DSSRILSGGE EGMVRVWRIG RTSQTLEASM KDHKGPVNCI RIKGS GDEC VSASSDGSCI LWDLHTFKRR TSLFANTFFK SVVYHPDESQ LVTAGTDRKV TYWDAYDGNA IRIIDGSDLD EVNALA VDR DGEALVSGGG DKLVKLWGYD EGHCYFVGVA HSGAITAVGV TPDKQRIVSV GTEGGIFIWD YQRPQTLADI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-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: 9528 / 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: 1.0 µm |
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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Output model | PDB-6ve7: |