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- EMDB-35792: GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin -

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Basic information

Entry
Database: EMDB / ID: EMD-35792
TitleGMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin
Map data
Sample
  • Complex: GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin
    • Protein or peptide: Tubulin alpha-4A chain
    • Protein or peptide: Tubulin beta-2A chain
    • Protein or peptide: Kinesin-1 heavy chain
  • Ligand: GUANOSINE-5'-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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / COPI-independent Golgi-to-ER retrograde traffic / regulation of modification of synapse structure, modulating synaptic transmission / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / plus-end-directed vesicle transport along microtubule / cytoplasm organization ...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 / COPI-independent Golgi-to-ER retrograde traffic / regulation of modification of synapse structure, modulating synaptic transmission / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / plus-end-directed vesicle transport along microtubule / cytoplasm organization / anterograde dendritic transport of neurotransmitter receptor complex / COPI-mediated anterograde transport / cytolytic granule membrane / Aggrephagy / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / anterograde neuronal dense core vesicle transport / Resolution of Sister Chromatid Cohesion / mitocytosis / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / retrograde neuronal dense core vesicle transport / RHO GTPases activate IQGAPs / Recycling pathway of L1 / anterograde axonal protein transport / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / 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 / Platelet degranulation / Regulation of PLK1 Activity at G2/M Transition / vesicle transport along microtubule / lysosome localization / MHC class II antigen presentation / positive regulation of potassium ion transport / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / ciliary rootlet / microtubule-based movement / stress granule disassembly / natural killer cell mediated cytotoxicity / synaptic vesicle transport / Insulin processing / postsynaptic cytosol / microtubule-based process / intercellular bridge / phagocytic vesicle / axon cytoplasm / dendrite cytoplasm / MHC class II antigen presentation / axon guidance / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cerebral cortex development / structural constituent of cytoskeleton / cellular response to type II interferon / centriolar satellite / mitotic spindle / Signaling by ALK fusions and activated point mutants / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nuclear membrane / vesicle / microtubule / hydrolase activity / cadherin binding / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / membrane / cytosol / cytoplasm
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-4A chain / Tubulin beta-2A chain
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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_35792.png

Downloads & links

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Map

FileDownload / File: emd_35792.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 512 pix.
= 674.816 Å		1.32 Å/pix.
x 512 pix.
= 674.816 Å		1.32 Å/pix.
x 512 pix.
= 674.816 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.0043911785 - 2.2383225
Average (Standard dev.)0.0065065925 (±0.06232918)
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_35792_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_35792_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin

EntireName: GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin
Components
  • Complex: GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin
    • Protein or peptide: Tubulin alpha-4A chain
    • Protein or peptide: Tubulin beta-2A chain
    • Protein or peptide: Kinesin-1 heavy chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: GMPCPP-Alpha4A/Beta2A-microtubule decorated with kinesin

SupramoleculeName: GMPCPP-Alpha4A/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-4A chain

MacromoleculeName: Tubulin alpha-4A 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: 50.806109 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: MRECISVHVG QAGVQMGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFTTFFC ETGAGKHVPR AVFVDLEPTV IDEIRNGPY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDPVLDRIR KLSDQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG ...String:
MRECISVHVG QAGVQMGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFTTFFC ETGAGKHVPR AVFVDLEPTV IDEIRNGPY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDPVLDRIR KLSDQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG KKSKLEFSIY PAPQVSTAVV EPYNSILTTH TTLEHSDCAF MVDNEAIYDI CRRNLDIERP TYTNLNRLIS QI VSSITAS LRFDGALNVD LTEFQTNLVP YPRIHFPLAT YAPVISAEKA YHEQLSVAEI TNACFEPANQ MVKCDPRHGK YMA CCLLYR GDVVPKDVNA AIAAIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHK FDLMY AKRAFVHWYV GEGMEEGEFS EAREDMAALE KDYEEVGIDS YEDEDEGEE

UniProtKB: Tubulin alpha-4A 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

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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

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8998

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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