+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35790 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / plus-end-directed vesicle transport along microtubule / cytoplasm organization / COPI-independent Golgi-to-ER retrograde traffic / cytolytic granule membrane / 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 / plus-end-directed vesicle transport along microtubule / cytoplasm organization / COPI-independent Golgi-to-ER retrograde traffic / cytolytic granule membrane / mitocytosis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / anterograde dendritic transport of neurotransmitter receptor complex / Aggrephagy / Kinesins / PKR-mediated signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / anterograde neuronal dense core vesicle transport / RHO GTPases activate IQGAPs / 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 / 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 / glial cell differentiation / AURKA Activation by TPX2 / vesicle transport along microtubule / forebrain morphogenesis / Regulation of PLK1 Activity at G2/M Transition / neuron projection arborization / lysosome localization / cerebellar cortex morphogenesis / positive regulation of potassium ion transport / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / centrosome cycle / stress granule disassembly / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / mitochondrion transport along microtubule / centrosome localization / ciliary rootlet / microtubule motor activity / natural killer cell mediated cytotoxicity / response to L-glutamate / kinesin complex / synaptic vesicle transport / smoothened signaling pathway / intercellular bridge / adult behavior / 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 / phagocytic vesicle / condensed chromosome / homeostasis of number of cells within a tissue / axon cytoplasm / MHC class II antigen presentation / cellular response to calcium ion / dendrite cytoplasm / neurogenesis / adult locomotory behavior / regulation of membrane potential / axon guidance / hippocampus development / positive regulation of synaptic transmission, GABAergic / locomotory behavior / intracellular protein transport / positive regulation of protein localization to plasma membrane / neuron migration / synapse organization / visual learning / neuromuscular junction / neuron differentiation / recycling endosome / cellular response to type II interferon / cerebral cortex development 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
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_35790.map.gz | 46.2 MB | EMDB map data format | |
---|---|---|---|---|
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 |
-Validation report
Summary document | emd_35790_validation.pdf.gz | 843.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_35790_full_validation.pdf.gz | 843.1 KB | Display | |
Data in XML | emd_35790_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_35790_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35790 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
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) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_35790_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_35790_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
Entire | Name: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin |
---|---|
Components |
|
-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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.9 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19287 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |