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- EMDB-35790: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin -

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Basic information

Entry
Database: EMDB / ID: EMD-35790
TitleGMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
Map data
Sample
  • Complex: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta-2A chain
    • Protein or peptide: Kinesin-1 heavy chainKinesin
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsmicrotubule / 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 / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / anterograde neuronal dense core vesicle transport / PKR-mediated signaling / COPI-mediated anterograde transport / anterograde dendritic transport of neurotransmitter receptor complex / mitocytosis / Aggrephagy / retrograde neuronal dense core vesicle transport / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / anterograde axonal protein transport / The role of GTSE1 in G2/M progression after G2 checkpoint / 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 / natural killer cell mediated cytotoxicity / MHC class II antigen presentation / pyramidal neuron differentiation / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / centrosome cycle / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / motor behavior / ciliary rootlet / centrosome localization / response to L-glutamate / synaptic vesicle transport / kinesin complex / microtubule motor activity / smoothened signaling pathway / adult behavior / regulation of synapse organization / intercellular bridge / microtubule-based movement / Insulin processing / startle response / microtubule polymerization / locomotory exploration behavior / centriolar satellite / Signaling by ALK fusions and activated point mutants / response to tumor necrosis factor / cytoplasmic microtubule / Nuclear events stimulated by ALK signaling in cancer / phagocytic vesicle / response to mechanical stimulus / homeostasis of number of cells within a tissue / axon cytoplasm / condensed chromosome / cellular response to calcium ion / MHC class II antigen presentation / regulation of membrane potential / dendrite cytoplasm / neurogenesis / adult locomotory behavior / locomotory behavior / axon guidance / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / synapse organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-1 heavy chain / Tubulin alpha-1A chain / Tubulin beta-2A chain
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZheng W / Zhao QY / Diao L / Bao L / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: 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
DepositionMar 31, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35790.png

Downloads & links

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Map

FileDownload / File: emd_35790.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.318 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.00721357 - 2.4771516
Average (Standard dev.)0.0063469238 (±0.060990147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 674.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35790_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35790_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin

EntireName: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
Components
  • Complex: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta-2A chain
    • Protein or peptide: Kinesin-1 heavy chainKinesin
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin

SupramoleculeName: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Tubulin alpha-1A chain

MacromoleculeName: 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 weightTheoretical: 51.01732 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: 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

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Macromolecule #2: Tubulin beta-2A chain

MacromoleculeName: Tubulin beta-2A chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.150961 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: 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

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Macromolecule #3: Kinesin-1 heavy chain

MacromoleculeName: Kinesin-1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.721066 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 9 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #5: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 9 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 9 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm 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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8998

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19287

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