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- PDB-9pnd: In situ microtubule of EpoB-induced regenerating axons -

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Basic information

Entry
Database: PDB / ID: 9pnd
TitleIn situ microtubule of EpoB-induced regenerating axons
Components
  • Detyrosinated tubulin alpha-1A chain
  • Tubulin beta-3 chain
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / microtubules / neuroregeneration / axon
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 / COPI-independent Golgi-to-ER retrograde traffic / netrin-activated signaling pathway / netrin receptor binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport ...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 / COPI-independent Golgi-to-ER retrograde traffic / netrin-activated signaling pathway / netrin receptor binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / Aggrephagy / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / Recycling pathway of L1 / dorsal root ganglion development / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / organelle transport along microtubule / 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 / forebrain morphogenesis / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / cerebellar cortex morphogenesis / glial cell differentiation / dentate gyrus development / neuron projection arborization / flagellated sperm motility / MHC class II antigen presentation / response to L-glutamate / pyramidal neuron differentiation / centrosome cycle / smoothened signaling pathway / regulation of synapse organization / startle response / adult behavior / motor behavior / response to tumor necrosis factor / locomotory exploration behavior / microtubule polymerization / response to mechanical stimulus / sperm flagellum / intercellular bridge / cytoplasmic microtubule / condensed chromosome / neurogenesis / peptide binding / homeostasis of number of cells within a tissue / axon guidance / cellular response to calcium ion / adult locomotory behavior / cell periphery / hippocampus development / filopodium / neuromuscular junction / locomotory behavior / intracellular protein transport / recycling endosome / synapse organization / cerebral cortex development / visual learning / structural constituent of cytoskeleton / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron migration / neuron differentiation / mitotic spindle / myelin sheath / lamellipodium / microtubule cytoskeleton / growth cone / neuron apoptotic process / gene expression / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / protein heterodimerization activity / axon / neuronal cell body / GTPase activity / synapse / dendrite / GTP binding / protein-containing complex binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
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
Chem-EPB / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1A chain / Tubulin beta-3 chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsBodakuntla, S. / Taira, K. / Yamada, Y. / Alvarez-Brecht, P. / Cada, A.K. / Basnet, N. / Zhang, R. / Martinez-Sanchez, A. / Biertumpfel, C. / Mizuno, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1ZIAHL006264 United States
CitationJournal: Nature / Year: 2025
Title: In situ structural mechanism of epothilone-B-induced CNS axon regeneration
Authors: Bodakuntla, S. / Taira, K. / Yamada, Y. / Alvarez-Brecht, P. / Cada, A.K. / Basnet, N. / Zhang, R. / Martinez-Sanchez, A. / Biertumpfel, C. / Mizuno, N.
History
DepositionJul 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tubulin beta-3 chain
D: Tubulin beta-3 chain
A: Detyrosinated tubulin alpha-1A chain
C: Detyrosinated tubulin alpha-1A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,35714
Polymers201,3124
Non-polymers3,04510
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, negative-staining EM, assay for oligomerization, absorbance at 400 nm
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 4 molecules BDAC

#1: Protein Tubulin beta-3 chain


Mass: 50467.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TUBB3 component of microtubules / Source: (natural) Mus musculus (house mouse) / Organ: Brain / Plasmid details: Axon / Tissue: Thalamus / References: UniProt: Q9ERD7
#2: Protein Detyrosinated tubulin alpha-1A chain


Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TUBA1A component of microtubules / Source: (natural) Mus musculus (house mouse) / Organ: Brain / Plasmid details: Axon / Tissue: Thalamus / References: UniProt: P68369

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Non-polymers , 5 types, 14 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-EPB / 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE / EPOTHILONE B


Mass: 507.683 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H41NO6S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Microtubule, axonal / Type: ORGANELLE OR CELLULAR COMPONENT
Details: from Epothilone B-induced regenerating explant axons from thalamus primary mouse embryo tissue after axotomy
Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Cellular location: Axon / Organ: Brain / Tissue: Thalamus
Buffer solutionpH: 7.2 / Details: Gibco Neurobasal Media
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: induced by axotomy in the presence of 1 nM Epothilone B
Specimen supportDetails: coated with poly-L-lysine and laminin / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1/4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 5 / Num. of real images: 4034 / Details: curated image number
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2SerialEMimage acquisition
4cryoSPARC4.5CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11cryoSPARC4.5initial Euler assignment
12cryoSPARC4.5final Euler assignment
13cryoSPARC4.5classification
14cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -27.64 ° / Axial rise/subunit: 9.695 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 399396
Details: picked in filament tracer with overlapping boxes with a step size of 82.5 Angstrom
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118551 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6dpu

6dpu


Accession code: 6dpu / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.19 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00114088
ELECTRON MICROSCOPYf_angle_d0.44219142
ELECTRON MICROSCOPYf_dihedral_angle_d10.6622044
ELECTRON MICROSCOPYf_chiral_restr0.0392092
ELECTRON MICROSCOPYf_plane_restr0.0032486

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