- EMDB-32033: 14pf microtubule decorated with EML1-GFP -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-32033
Title
14pf microtubule decorated with EML1-GFP
Map data
Refined map of 14pf microtubule bound to EML1-GFP
Sample
Complex: Complex of microtubule with HEK293 cell lysate containing over expressed EML1-GFP
Protein or peptide: Tubulin alpha-1B chain
Protein or peptide: Tubulin beta chain
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 / natural killer cell mediated cytotoxicity / Assembly and cell surface presentation of NMDA receptors / Kinesins / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / Recycling pathway of L1 / cytoplasmic microtubule / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / spindle assembly / cellular response to interleukin-4 / Hedgehog 'off' state / 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 / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / mitotic spindle / cytoplasmic ribonucleoprotein granule / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / double-stranded RNA binding / 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 / protein-containing complex binding / GTP binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function
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
Deposition
Oct 7, 2021
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Header (metadata) release
Dec 1, 2021
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Map release
Dec 1, 2021
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Update
Dec 13, 2023
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Current status
Dec 13, 2023
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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
Components
Complex: Complex of microtubule with HEK293 cell lysate containing over expressed EML1-GFP
Protein or peptide: Tubulin alpha-1B chain
Protein or peptide: Tubulin beta chain
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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
Source (natural)
Organism: Homo sapiens (human)
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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
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
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
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
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