+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3522 | |||||||||
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Title | S. pombe microtubule copolymerized with GTP and Mal3-143 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / nuclear migration by microtubule mediated pushing forces / cortical microtubule / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule ...mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / nuclear migration by microtubule mediated pushing forces / cortical microtubule / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule / nuclear division / mitotic spindle elongation / nuclear microtubule / mitotic spindle midzone / protein localization to microtubule / mitotic spindle pole body / astral microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule organizing center / microtubule lateral binding / intracellular distribution of mitochondria / cytoplasmic microtubule / ATPase activator activity / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / cytoplasmic microtubule organization / molecular condensate scaffold activity / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / response to antibiotic / GTPase activity / GTP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | von Loeffelholz O / Moores C | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2017 Title: Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics. Authors: Ottilie von Loeffelholz / Neil A Venables / Douglas Robert Drummond / Miho Katsuki / Robert Cross / Carolyn A Moores / Abstract: Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo- ...Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces. A 4.6-Å resolution structure of microtubule-bound Mal3 shows that Mal3 makes a distinctive footprint on the S. pombe microtubule lattice and that unlike mammalian microtubules, S. pombe microtubules do not show the longitudinal lattice compaction associated with EB protein binding and GTP hydrolysis. Our results firmly support a structural plasticity view of microtubule dynamics in which microtubule lattice conformation is sensitive to a variety of effectors and differently so for different tubulins. | |||||||||
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_3522.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-3522-v30.xml emd-3522.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_3522.png | 238.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3522 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3522 | HTTPS FTP |
-Validation report
Summary document | emd_3522_validation.pdf.gz | 251.2 KB | Display | EMDB validaton report |
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Full document | emd_3522_full_validation.pdf.gz | 250.3 KB | Display | |
Data in XML | emd_3522_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3522 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3522 | HTTPS FTP |
-Related structure data
Related structure data | 5mjsMC 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_3522.map.gz / Format: CCP4 / Size: 9.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 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 decorated with Mal3
Entire | Name: Microtubule decorated with Mal3 |
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Components |
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-Supramolecule #1: Microtubule decorated with Mal3
Supramolecule | Name: Microtubule decorated with Mal3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
Recombinant expression | Organism: Schizosaccharomyces pombe (fission yeast) |
-Macromolecule #1: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 47.191031 KDa |
Recombinant expression | Organism: Schizosaccharomyces pombe (fission yeast) |
Sequence | String: MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS ...String: MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS VAPAPKSSDT VVEPYNATLS MHQLVENSDE TFCIDNEALS SIFANTLKIK SPSYDDLNHL VSAVMAGVTT SF RFPGELN SDLRKLAVNM VPFPRLHFFM VGFAPLAAIG SSSFQAVSVP ELTQQMFDAN NMMVAADPRH GRYLTVAALF RGK VSMKEV DEQIRSVQTK NSAYFVEWIP DNVLKAVCSV PPKDLKMSAT FIGNSTSIQE IFRRLGDQFS AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QEAG |
-Macromolecule #2: Microtubule integrity protein mal3
Macromolecule | Name: Microtubule integrity protein mal3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 16.6689 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSESRQELLA WINQVTSLGL TRIEDCGKGY AMIQIFDSIY QDIPLKKVNF ECNNEYQYIN NWKVLQQVFL KKGIDKVVDP ERLSRCKMQ DNLEFVQWAK RFWDQYYPGG DYDALARRGN RGPANTRVMN SSAGATGPSR RRQV |
-Macromolecule #3: Tubulin alpha-1 chain
Macromolecule | Name: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 |
Molecular weight | Theoretical: 49.813832 KDa |
Recombinant expression | Organism: Schizosaccharomyces pombe (fission yeast) |
Sequence | String: MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK ...String: MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK SNLQFSVYPA PQVSTSVVEP YNSVLTTHAT LDNSDCTFMV DNEACYDICR RNLDIERPTY ENLNRLIAQV VS SITASLR FAGSLNVDLN EFQTNLVPYP RIHFPLVTYS PIVSAAKAFH ESNSVQEITN QCFEPYNQMV KCDPRTGRYM ATC LLYRGD VIPRDVQAAV TSIKSRRTIQ FVDWCPTGFK IGICYEPPQH VPGSGIAKVN RAVCMLSNTT SIAEAWSRLD HKFD LMYSK RAFVHWYVGE GMEEGEFSEA REDLAALERD YEEVGQDSM |
-Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GDP |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: GTP |
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Source (natural) | Organism: Schizosaccharomyces pombe (fission yeast) |
Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 6.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | PDB-5mjs: |