+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9004 | ||||||||||||
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Title | Cryo-EM structure of C. elegans GDP-microtubule | ||||||||||||
Map data | Cryo-EM structure of C. elegans GDP-microtubules | ||||||||||||
Sample |
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Keywords | Cytoskeletal protein / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex ...COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / meiotic spindle organization / embryo development ending in birth or egg hatching / centrosome localization / tubulin complex / establishment of mitotic spindle orientation / regulation of cytokinesis / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / protein localization / mitotic cell cycle / microtubule / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||
Authors | Chaaban S / Jariwala S | ||||||||||||
Funding support | Canada, 3 items
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Citation | Journal: Dev Cell / Year: 2018 Title: The Structure and Dynamics of C. elegans Tubulin Reveals the Mechanistic Basis of Microtubule Growth. Authors: Sami Chaaban / Shashank Jariwala / Chieh-Ting Hsu / Stefanie Redemann / Justin M Kollman / Thomas Müller-Reichert / David Sept / Khanh Huy Bui / Gary J Brouhard / Abstract: The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and ...The dynamic instability of microtubules is a conserved and fundamental mechanism in eukaryotes. Yet microtubules from different species diverge in their growth rates, lattice structures, and responses to GTP hydrolysis. Therefore, we do not know what limits microtubule growth, what determines microtubule structure, or whether the mechanisms of dynamic instability are universal. Here, we studied microtubules from the nematode C. elegans, which have strikingly fast growth rates and non-canonical lattices in vivo. Using a reconstitution approach, we discovered that C. elegans microtubules combine intrinsically fast growth with very frequent catastrophes. We solved the structure of C. elegans microtubules to 4.8 Å and discovered sequence divergence in the lateral contact loops, one of which is ordered in C. elegans but unresolved in other species. We provide direct evidence that C. elegans tubulin has a higher free energy in solution and propose a model wherein the ordering of lateral contact loops activates tubulin for growth. | ||||||||||||
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_9004.map.gz | 35.7 MB | EMDB map data format | |
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Header (meta data) | emd-9004-v30.xml emd-9004.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9004_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_9004.png | 315.4 KB | ||
Filedesc metadata | emd-9004.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9004 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9004 | HTTPS FTP |
-Validation report
Summary document | emd_9004_validation.pdf.gz | 695.1 KB | Display | EMDB validaton report |
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Full document | emd_9004_full_validation.pdf.gz | 694.6 KB | Display | |
Data in XML | emd_9004_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_9004_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9004 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9004 | HTTPS FTP |
-Related structure data
Related structure data | 6e88MC M: atomic model generated by this map C: citing same article (ref.) |
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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_9004.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of C. elegans GDP-microtubules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.373 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 : microtubule
Entire | Name: microtubule |
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Components |
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-Supramolecule #1: microtubule
Supramolecule | Name: microtubule / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: C. elegans microtubules polymerized in the presence of GTP |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 |
Molecular weight | Theoretical: 165 kDa/nm |
-Macromolecule #1: Tubulin alpha-2 chain
Macromolecule | Name: Tubulin alpha-2 chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 |
Molecular weight | Theoretical: 48.467609 KDa |
Sequence | String: MREVISIHVG QAGVQIGNAC WELYCLEHGI QPDGTMPTQS TNEGESFTTF FSDTGSGRYV PRSIFVDLEP TVVDEIRTGT YKKLFHPEQ MITGKEDAAN NYARGHYTVG KELIDTVLDR IRRLADNCSG LQGFFVFHSF GGGTGSGFTS LLMERLSVDY G KKSKLEFS ...String: MREVISIHVG QAGVQIGNAC WELYCLEHGI QPDGTMPTQS TNEGESFTTF FSDTGSGRYV PRSIFVDLEP TVVDEIRTGT YKKLFHPEQ MITGKEDAAN NYARGHYTVG KELIDTVLDR IRRLADNCSG LQGFFVFHSF GGGTGSGFTS LLMERLSVDY G KKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDVE RPSYTNLNRI ISQVVSSITA SL RFDGALN VDLNEFQTNL VPYPRIHFPL AAYTPLISAE KAYHEALSVS DITNSCFEPA NQMVKCDPRH GKYMAVCLLY RGD VVPKDV NTAIAAIKTK RTIQFVDWCP TGFKVGINYQ PPTVVPGGDL AKVPRAVCML SNTTAIAEAW SRLDYKFDLM YAKR AFVHW YVGEGMEEGE FTEAREDLAA LEKDYEEVG UniProtKB: Tubulin alpha-2 chain |
-Macromolecule #2: Tubulin beta-2 chain
Macromolecule | Name: Tubulin beta-2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 |
Molecular weight | Theoretical: 47.843988 KDa |
Sequence | String: MREIVHVQAG QCGNQIGSKF WEVISDEHGI QPDGTFKGET DLQLERIDVY YNEANNGKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN FVFGQSGAGN NWAKGHYTEG AELVDNVLDV IRKEAEGCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMSSFS ...String: MREIVHVQAG QCGNQIGSKF WEVISDEHGI QPDGTFKGET DLQLERIDVY YNEANNGKYV PRAVLVDLEP GTMDSVRSGP FGQLFRPDN FVFGQSGAGN NWAKGHYTEG AELVDNVLDV IRKEAEGCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMSSFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICYRTLKLT NPTYGDLNHL VSLTMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLSAKG TQAYRALTVA ELTQQMFDAK NMMAACDPRH GRYLTVAAMF RGR MSMREV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAAT FVGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLISEYQQY Q UniProtKB: Tubulin beta-2 chain |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / 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: 6.9 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 29.33 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-6e88: |