+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35790 | |||||||||
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Title | GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | microtubule / tubulin isotype / cryo-EM structure / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / mitocytosis ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / mitocytosis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / PKR-mediated signaling / COPI-mediated anterograde transport / anterograde dendritic transport of neurotransmitter receptor complex / Aggrephagy / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / The role of GTSE1 in G2/M progression after G2 checkpoint / retrograde neuronal dense core vesicle transport / Recycling pathway of L1 / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / organelle transport along microtubule / glial cell differentiation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / vesicle transport along microtubule / forebrain morphogenesis / neuron projection arborization / Regulation of PLK1 Activity at G2/M Transition / lysosome localization / cerebellar cortex morphogenesis / positive regulation of potassium ion transport / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / natural killer cell mediated cytotoxicity / RHO GTPases activate KTN1 / Kinesins / plus-end-directed microtubule motor activity / stress granule disassembly / centrosome cycle / mitochondrion transport along microtubule / motor behavior / ciliary rootlet / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / response to L-glutamate / synaptic vesicle transport / kinesin complex / smoothened signaling pathway / adult behavior / intercellular bridge / regulation of synapse organization / Insulin processing / microtubule-based movement / startle response / cytoplasmic microtubule / locomotory exploration behavior / microtubule polymerization / centriolar satellite / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / axon cytoplasm / homeostasis of number of cells within a tissue / phagocytic vesicle / cellular response to calcium ion / MHC class II antigen presentation / dendrite cytoplasm / neurogenesis / adult locomotory behavior / locomotory behavior / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / axon guidance / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / synapse organization / intracellular protein transport / neuron migration / visual learning / Signaling by ALK fusions and activated point mutants / neuromuscular junction / neuron differentiation / recycling endosome Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zheng W / Zhao QY / Diao L / Bao L / Cong Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Acta Biochim Biophys Sin (Shanghai) / Year: 2023 Title: Cryo-EM of α-tubulin isotype-containing microtubules revealed a contracted structure of α4A/β2A microtubules. Authors: Lei Diao / Wei Zheng / Qiaoyu Zhao / Mingyi Liu / Zhenglin Fu / Xu Zhang / Lan Bao / Yao Cong / Abstract: Microtubules are hollow α/β-tubulin heterodimeric polymers that play critical roles in cells. In vertebrates, both α- and β-tubulins have multiple isotypes encoded by different genes, which are ...Microtubules are hollow α/β-tubulin heterodimeric polymers that play critical roles in cells. In vertebrates, both α- and β-tubulins have multiple isotypes encoded by different genes, which are intrinsic factors in regulating microtubule functions. However, the structures of microtubules composed of different tubulin isotypes, especially α-tubulin isotypes, remain largely unknown. Here, we purify recombinant tubulin heterodimers composed of different mouse α-tubulin isotypes, including α1A, α1C and α4A, with the β-tubulin isotype β2A. We further assemble and determine the cryo-electron microscopy (cryo-EM) structures of α1A/β2A, α1C/β2A, and α4A/β2A microtubules. Our structural analysis demonstrates that α4A/β2A microtubules exhibit longitudinal contraction between tubulin interdimers compared with α1A/β2A and α1C/β2A microtubules. Collectively, our findings reveal that α-tubulin isotype composition can tune microtubule structures, and also provide evidence for the "tubulin code" hypothesis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35790.map.gz | 46.2 MB | EMDB map data format | |
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Header (meta data) | emd-35790-v30.xml emd-35790.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_35790.png | 68.7 KB | ||
Filedesc metadata | emd-35790.cif.gz | 6.5 KB | ||
Others | emd_35790_half_map_1.map.gz emd_35790_half_map_2.map.gz | 146.5 MB 146.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35790 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35790 | HTTPS FTP |
-Related structure data
Related structure data | 8ixaMC 8ixbMC 8ixdC 8ixeC 8ixfC 8ixgC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35790.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35790_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35790_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
Entire | Name: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin |
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Components |
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-Supramolecule #1: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
Supramolecule | Name: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Tubulin alpha-1A chain
Macromolecule | Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 Details: Author stated: the data processing is a non-standard procedure for microtubule-type of helical reconstruction with a seam, and it was performed around 2017 to 2019. We followed the procedure ...Details: Author stated: the data processing is a non-standard procedure for microtubule-type of helical reconstruction with a seam, and it was performed around 2017 to 2019. We followed the procedure developed by Dr. Rui Zhang (R. Zhang, Cell, 2015, doi: 10.1016/j.cell.2015.07.012), with all the scripts provided by him. In this way, the generated half-maps have an applied circular mask but without touching the structural outer boundaries. Number of copies: 9 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 51.01732 KDa |
Recombinant expression | Organism: Insecta environmental sample (insect) |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFNTFFS ETGAGKHVPR AVFVDLEPTV IDEVRTGTY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDLVLDRIR KLADQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFNTFFS ETGAGKHVPR AVFVDLEPTV IDEVRTGTY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDLVLDRIR KLADQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG KKSKLEFSIY PAPQVSTAVV EPYNSILTTH TTLEHSDCAF MVDNEAIYDI CRRNLDIERP TYTNLNRLIG QI VSSITAS LRFDGALNVD LTEFQTNLVP YPRIHFPLAT YAPVISAEKA YHEQLSVAEI TNACFEPANQ MVKCDPRHGK YMA CCLLYR GDVVPKDVNA AIATIKTKRT IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHK FDLMY AKRAFVHWYV GEGMEEGEFS EAREDMAALE KDYEEVGVDS VEGEGEEEGE EY UniProtKB: Tubulin alpha-1A chain |
-Macromolecule #2: Tubulin beta-2A chain
Macromolecule | Name: Tubulin beta-2A chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 51.150961 KDa |
Recombinant expression | Organism: Insecta environmental sample (insect) |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYSIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA GGSGGDYKDD DK UniProtKB: Tubulin beta-2A chain |
-Macromolecule #3: Kinesin-1 heavy chain
Macromolecule | Name: Kinesin-1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.721066 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMADLAEC NIKVMCRFRP LNESEVNRGD KYIAKFQGED TVVIASKPYA FDRVFQSSTS QEQVYNDCA KKIVKDVLEG YNGTIFAYGQ TSSGKTHTME GKLHDPEGMG IIPRIVQDIF NYIYSMDENL EFHIKVSYFE I YLDKIRDL ...String: MGSSHHHHHH SSGLVPRGSH MASMADLAEC NIKVMCRFRP LNESEVNRGD KYIAKFQGED TVVIASKPYA FDRVFQSSTS QEQVYNDCA KKIVKDVLEG YNGTIFAYGQ TSSGKTHTME GKLHDPEGMG IIPRIVQDIF NYIYSMDENL EFHIKVSYFE I YLDKIRDL LDVSKTNLSV HEDKNRVPYV KGCTERFVCS PDEVMDTIDE GKSNRHVAVT NMNEHSSRSH SIFLINVKQE NT QTEQKLS GKLYLVDLAG SAKVSKTGAE GAVLDEAKNI NKSLSALGNV ISALAEGSTY VPYRDSKMTR ILQDSLGGNC RTT IVICCS PSSYNESETK STLLFGQRAK TIKNTVCVNV ELTAEQWKKK YEKEKE UniProtKB: Kinesin-1 heavy chain |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 9 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 9 / Formula: G2P |
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Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ChemComp-G2P: |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 9 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 36.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19287 |