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- EMDB-45592: 13-pf microtubule from the LRRK2(I2020T) and MLi-2 dataset -

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Basic information

Entry
Database: EMDB / ID: EMD-45592
Title13-pf microtubule from the LRRK2(I2020T) and MLi-2 dataset
Map data
Sample
  • Complex: Microtubules from LRRK2(I2020T)+MLi-2 dataset
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
KeywordsMicrutubules / tubulins / STRUCTURAL PROTEIN
Function / homology
Function and homology information


odontoblast differentiation / Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III ...odontoblast differentiation / Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cerebellar cortex morphogenesis / glial cell differentiation / neuron projection arborization / dentate gyrus development / Formation of tubulin folding intermediates by CCT/TriC / flagellated sperm motility / Gap junction assembly / Kinesins / Prefoldin mediated transfer of substrate to CCT/TriC / pyramidal neuron differentiation / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / GTPase activating protein binding / response to L-glutamate / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / smoothened signaling pathway / nuclear envelope lumen / regulation of synapse organization / startle response / motor behavior / Recycling pathway of L1 / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / MHC class I protein binding / response to mechanical stimulus / sperm flagellum / microtubule-based process / RHO GTPases activate IQGAPs / intercellular bridge / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / homeostasis of number of cells within a tissue / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / RHO GTPases Activate Formins / intracellular protein transport / cerebral cortex development / PKR-mediated signaling / synapse organization / visual learning / structural constituent of cytoskeleton / recycling endosome / microtubule cytoskeleton organization / neuron migration / memory / HCMV Early Events / Aggrephagy / cytoplasmic ribonucleoprotein granule / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / azurophil granule lumen / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / cell body / neuron apoptotic process / gene expression / Potential therapeutics for SARS / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoskeleton / microtubule / cilium / membrane raft / protein heterodimerization activity / protein domain specific binding / cell division / hydrolase activity / GTPase activity / Neutrophil degranulation
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
Similarity search - Domain/homology
Tubulin beta chain / Tubulin alpha-1A chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 5.9 Å
AuthorsChen S / Leschziner AE / Villa E
Funding support United States, 2 items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000519 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2024
Title: Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2
Authors: Chen S / Basiashvili T / Hutchings J / Sanz Murillo M / Villagran Suarez A / Alegrio Louro J / Leschziner AE / Villa E
History
DepositionJul 1, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45592.png

Downloads & links

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Map

FileDownload / File: emd_45592.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 264 pix.
= 570.504 Å		2.16 Å/pix.
x 264 pix.
= 570.504 Å		2.16 Å/pix.
x 264 pix.
= 570.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.161 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.1836358 - 2.8207915
Average (Standard dev.)0.06768023 (±0.21707718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 570.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45592_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45592_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 : Microtubules from LRRK2(I2020T)+MLi-2 dataset

EntireName: Microtubules from LRRK2(I2020T)+MLi-2 dataset
Components
  • Complex: Microtubules from LRRK2(I2020T)+MLi-2 dataset
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain

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Supramolecule #1: Microtubules from LRRK2(I2020T)+MLi-2 dataset

SupramoleculeName: Microtubules from LRRK2(I2020T)+MLi-2 dataset / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / 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)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL IGQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRT IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQVFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMAVTFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA EEEEDFGEEA EEEA

UniProtKB: Tubulin beta chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

Concentration1.43 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
80.0 mMsodium chlorideNaCl
0.5 mMTCEP
2.5 mMmagnesium chlorideMgCl2
10.0 uMTAXOL
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 90.0 K
SoftwareName: SerialEM (ver. 4.6)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number real images: 1 / Average exposure time: 0.65 sec. / Average electron dose: 3.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.5 µm / Calibrated defocus min: 3.5 µm / Calibrated magnification: 42000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 9.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 6487
ExtractionNumber tomograms: 131 / Number images used: 65612 / Reference model: EMD-5193 / Method: 3D classification / Software - Name: Dynamo
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 6 / Avg.num./class: 6000 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. 1.7)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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