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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 / 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 ...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 / embryonic brain development / flagellated sperm motility / Gap junction assembly / Kinesins / positive regulation of axon guidance / 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 / response to L-glutamate / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / regulation of synapse organization / startle response / motor behavior / Recycling pathway of L1 / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / 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 / 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 / homeostasis of number of cells within a tissue / Mitotic Prometaphase / cellular response to calcium ion / EML4 and NUDC in mitotic spindle formation / 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 / RHO GTPases Activate Formins / intracellular protein transport / cerebral cortex development / PKR-mediated signaling / synapse organization / visual learning / recycling endosome / structural constituent of cytoskeleton / modulation of chemical synaptic transmission / microtubule cytoskeleton organization / Schaffer collateral - CA1 synapse / neuron migration / memory / HCMV Early Events / Aggrephagy / cytoplasmic ribonucleoprotein granule / 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: Nat Struct Mol Biol / Year: 2026
Title: Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state.
Authors: Elena A Zehr / Shufeng Sun / Stephanie L Sarbanes / Antonina Roll-Mecak /
Abstract: Microtubules scaffold cells, supporting signaling and cargo transport. They assemble from GTP-tubulin, which hydrolyzes to GDP-tubulin during polymerization. GTP-microtubule lattices are stable; GDP ...Microtubules scaffold cells, supporting signaling and cargo transport. They assemble from GTP-tubulin, which hydrolyzes to GDP-tubulin during polymerization. GTP-microtubule lattices are stable; GDP lattices depolymerize rapidly. In vitro, hydrolysis triggers lattice compaction. Lattice spacing regulates motors and microtubule-associated proteins; however, the conformation of tubulin in microtubules in cells is unknown. Here, we present the atomic-resolution cryo-electron microscopy structure of human microtubules in situ, in the axons of human cortical neurons derived from induced pluripotent stem cells (iPS cells). Our 2.7-Å-resolution reconstruction delineates bound water molecules and reveals that axonal microtubules adopt an expanded GTP-like lattice, despite being GDP bound. Using cryo-electron tomography and power spectrum analysis, we find that, unlike in axons, microtubules in undifferentiated iPS cells are compacted. Therefore, lattice expansion is part of neuronal differentiation. Our work provides molecular insights into neurogenesis and has implications for understanding microtubule stability and effector recruitment in neurons.
History
DepositionJun 3, 2025Deposition site: RCSB / Processing site: RCSB
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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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