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- PDB-8ixb: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ixb | ||||||
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Title | GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region | ||||||
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![]() | STRUCTURAL PROTEIN / microtubule / tubulin isotype / cryo-EM structure | ||||||
Function / homology | ![]() 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 / natural killer cell mediated cytotoxicity / pyramidal neuron differentiation / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / centrosome cycle / motor behavior / mitochondrion transport along microtubule / ciliary rootlet / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / response to L-glutamate / kinesin complex / synaptic vesicle transport / smoothened signaling pathway / adult behavior / intercellular bridge / regulation of synapse organization / Insulin processing / microtubule-based movement / startle response / locomotory exploration behavior / microtubule polymerization / cytoplasmic microtubule / centriolar satellite / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / axon cytoplasm / cellular response to calcium ion / MHC class II antigen presentation / dendrite cytoplasm / phagocytic vesicle / adult locomotory behavior / neurogenesis / locomotory behavior / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / synapse organization / axon guidance / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / neuron differentiation / recycling endosome / structural constituent of cytoskeleton Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
![]() | Zheng, W. / Zhao, Q.Y. / Diao, L. / Bao, L. / Cong, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 822.8 KB | Display | ![]() |
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PDB format | ![]() | 674.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 131.1 KB | Display | |
Data in CIF | ![]() | 193.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35790MC ![]() 8ixaC ![]() 8ixdC ![]() 8ixeC ![]() 8ixfC ![]() 8ixgC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 12 molecules HAEFWQUVlgkm
#1: Protein | Mass: 51017.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68369, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Protein | Mass: 51150.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 41721.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 12 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/ATP.gif)
#4: Chemical | ChemComp-GTP / #5: Chemical | ChemComp-G2P / #6: Chemical | ChemComp-ATP / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19287 / Symmetry type: POINT |