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- PDB-9ox7: In situ microtubule structure in the axon of a human neuron -

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Basic information

Entry
Database: PDB / ID: 9ox7
TitleIn situ microtubule structure in the axon of a human neuron
Components
  • Tubulin alpha-1A chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / Human in-situ microtubule / axon / cytoskeleton
Function / homology
Function and homology information


Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport ...Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / 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 / Formation of tubulin folding intermediates by CCT/TriC / glial cell differentiation / dentate gyrus development / neuron projection arborization / embryonic brain development / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / positive regulation of axon guidance / Assembly and cell surface presentation of NMDA receptors / pyramidal neuron differentiation / response to L-glutamate / COPI-independent Golgi-to-ER retrograde traffic / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / regulation of synapse organization / startle response / motor behavior / microtubule polymerization / Recycling pathway of L1 / locomotory exploration behavior / response to tumor necrosis factor / response to mechanical stimulus / sperm flagellum / microtubule-based process / RHO GTPases activate IQGAPs / Hedgehog 'off' state / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / 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 / homeostasis of number of cells within a tissue / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / intracellular protein transport / RHO GTPases Activate Formins / cerebral cortex development / synapse organization / PKR-mediated signaling / visual learning / recycling endosome / structural constituent of cytoskeleton / modulation of chemical synaptic transmission / microtubule cytoskeleton organization / Schaffer collateral - CA1 synapse / neuron migration / memory / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / neuron apoptotic process / gene expression / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / cell division / hydrolase activity / GTPase activity / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome / metal ion binding / identical protein binding / nucleus / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1A chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZehr, E.A. / Sun, S. / Roll-Mecak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1ZIANS003164 United States
CitationJournal: To Be Published
Title: Microtubules in the axon are GDP-bound but adopt a stable GTP-like expanded state
Authors: Zehr, E.A. / Sun, S. / Sarbanes, S.L. / Roll-Mecak, A.
History
DepositionJun 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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-2B chain
D: Tubulin beta-2B chain
E: Tubulin beta-2B chain
F: Tubulin beta-2B chain
A: Tubulin alpha-1A chain
C: Tubulin alpha-1A chain
G: Tubulin alpha-1A chain
H: Tubulin alpha-1A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,71620
Polymers400,7538
Non-polymers3,96312
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 8 molecules BDEFACGH

#1: Protein
Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: WTC11 / Tissue: Neuronal / References: UniProt: Q9BVA1
#2: Protein
Tubulin alpha-1A chain / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


Mass: 50188.441 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: WTC11 / Tissue: Neuronal / References: UniProt: Q71U36

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Non-polymers , 4 types, 44 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: Axonal alpha1A and betaIIB microtubule / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: axon / Tissue: neuronal
Buffer solutionpH: 7.2
SpecimenConc.: 0.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 303 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: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 2.03 sec. / Electron dose: 56.57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 6 / Num. of real images: 3017
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2SerialEMimage acquisition
4cryoSPARC4CTF correction
7ISOLDE1.6model fitting
8Coot0.9.8.91model fitting
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
13cryoSPARC43D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -27.6723 ° / Axial rise/subunit: 9.60742 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 288841
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1887666 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingB value: 69 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation
Atomic model buildingPDB-ID: 8v4k

8v4k


Accession code: 8v4k / Source name: PDB / Type: experimental model

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