+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32033 | ||||||||||||
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Title | 14pf microtubule decorated with EML1-GFP | ||||||||||||
Map data | Refined map of 14pf microtubule bound to EML1-GFP | ||||||||||||
Sample |
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Keywords | Cytoskeleton / Echinoderm microtubule-associated protein-like 1 (EML1) / Microtubule associated protein (MAP) / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | Function and homology information odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly ...odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / cytoplasmic microtubule / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / spindle assembly / cellular response to interleukin-4 / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / PKR-mediated signaling / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / cell body / microtubule / Potential therapeutics for SARS / cytoskeleton / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Bangera M / Sirajuddin M | ||||||||||||
Funding support | 3 items
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Citation | Journal: Nat Cell Biol / Year: 2022 Title: Lysate-based pipeline to characterize microtubule-associated proteins uncovers unique microtubule behaviours. Authors: A S Jijumon / Satish Bodakuntla / Mariya Genova / Mamata Bangera / Violet Sackett / Laetitia Besse / Fatlinda Maksut / Veronique Henriot / Maria M Magiera / Minhajuddin Sirajuddin / Carsten Janke / Abstract: The microtubule cytoskeleton forms complex macromolecular assemblies with a range of microtubule-associated proteins (MAPs) that have fundamental roles in cell architecture, division and motility. ...The microtubule cytoskeleton forms complex macromolecular assemblies with a range of microtubule-associated proteins (MAPs) that have fundamental roles in cell architecture, division and motility. Determining how an individual MAP modulates microtubule behaviour is an important step in understanding the physiological roles of various microtubule assemblies. To characterize how MAPs control microtubule properties and functions, we developed an approach allowing for medium-throughput analyses of MAPs in cell-free conditions using lysates of mammalian cells. Our pipeline allows for quantitative as well as ultrastructural analyses of microtubule-MAP assemblies. Analysing 45 bona fide and potential mammalian MAPs, we uncovered previously unknown activities that lead to distinct and unique microtubule behaviours such as microtubule coiling or hook formation, or liquid-liquid phase separation along the microtubule lattice that initiates microtubule branching. We have thus established a powerful tool for a thorough characterization of a wide range of MAPs and MAP variants, thus opening avenues for the determination of mechanisms underlying their physiological roles and pathological implications. | ||||||||||||
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_32033.map.gz | 296.7 MB | EMDB map data format | |
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Header (meta data) | emd-32033-v30.xml emd-32033.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32033_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_32033.png | 184 KB | ||
Masks | emd_32033_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-32033.cif.gz | 6.1 KB | ||
Others | emd_32033_additional_1.map.gz emd_32033_half_map_1.map.gz emd_32033_half_map_2.map.gz | 292.1 MB 258.4 MB 257.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32033 | HTTPS FTP |
-Validation report
Summary document | emd_32033_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_32033_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_32033_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | emd_32033_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32033 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32033.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Refined map of 14pf microtubule bound to EML1-GFP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_32033_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: 15 Angstroms low pass filtered map of 14pf...
File | emd_32033_additional_1.map | ||||||||||||
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Annotation | 15 Angstroms low pass filtered map of 14pf microtubule bound to EML1-GFP | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 14pf microtubule bound to EML1-GFP-half map 1 (unfiltered)
File | emd_32033_half_map_1.map | ||||||||||||
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Annotation | 14pf microtubule bound to EML1-GFP-half map 1 (unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 14pf microtubule bound to EML1-GFP-half map 2 (unfiltered)
File | emd_32033_half_map_2.map | ||||||||||||
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Annotation | 14pf microtubule bound to EML1-GFP-half map 2 (unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of microtubule with HEK293 cell lysate containing over ex...
Entire | Name: Complex of microtubule with HEK293 cell lysate containing over expressed EML1-GFP |
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Components |
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-Supramolecule #1: Complex of microtubule with HEK293 cell lysate containing over ex...
Supramolecule | Name: Complex of microtubule with HEK293 cell lysate containing over expressed EML1-GFP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 Details: The reconstruction contains a mix of tubulin from goat brain (nucleating seeds) and tubulin from HEK293 cellular lysate so will have a mixture of both sequences. Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIATI KTKRSIQFVD WCPTGFKVGI NYQPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGVDSVEGE GEEEGEEY UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 Details: The reconstruction contains a mix of tubulin from goat brain (nucleating seeds) and tubulin from HEK293 cellular lysate so will have a mixture of both sequences. Sequence of goat brain beta ...Details: The reconstruction contains a mix of tubulin from goat brain (nucleating seeds) and tubulin from HEK293 cellular lysate so will have a mixture of both sequences. Sequence of goat brain beta tubulin can be accessed using Uniprot ID A0A452G3J7 Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKEAESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKEAESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VVPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQVFDA KNMM AACDP RHGRYLTVAA VFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMA VTFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQDATAEEE EDFGEEAEEE A UniProtKB: Tubulin beta chain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 6.8 / Component - Formula: BRB80 Details: 80mM PIPES, 2mM MgCl2, 1mM EGTA supplemented with 1mM GMPCPP |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: GMPCPP MT seeds in warm BRB80 applied to the grid followed by second application of pre-warmed lysate containing over expressed EML1-GFP. After an incubation time of 20 seconds, grid blotted ...Details: GMPCPP MT seeds in warm BRB80 applied to the grid followed by second application of pre-warmed lysate containing over expressed EML1-GFP. After an incubation time of 20 seconds, grid blotted for 3 seconds before plunging into liquid ethane.. |
Details | Goat brain tubulin was polymerized with 1mM GMPCPP at 310K for 2 hours, spun on warm 50 percent BRB80 sucrose cushion and resuspended in twice the volume of warm BRB80 buffer |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1143 / Average exposure time: 1.5 sec. / Average electron dose: 44.17 e/Å2 / Details: 30 frames |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 101449 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / 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 |