[English] 日本語
Yorodumi
- PDB-9ox7: In situ microtubule structure in the axon of a human neuron -

+
Open data


ID or keywords:

Loading...

-
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


Cilium Assembly / Cargo trafficking to the periciliary membrane / Post-chaperonin tubulin folding pathway / axonemal microtubule / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / organelle transport along microtubule / forebrain morphogenesis / glial cell differentiation ...Cilium Assembly / Cargo trafficking to the periciliary membrane / Post-chaperonin tubulin folding pathway / axonemal microtubule / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / organelle transport along microtubule / forebrain morphogenesis / glial cell differentiation / cerebellar cortex morphogenesis / dentate gyrus development / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / Formation of tubulin folding intermediates by CCT/TriC / embryonic brain development / Gap junction assembly / smoothened signaling pathway / pyramidal neuron differentiation / motor behavior / Kinesins / positive regulation of axon guidance / Prefoldin mediated transfer of substrate to CCT/TriC / response to L-glutamate / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / 'de novo' protein folding / startle response / flagellated sperm motility / intercellular bridge / regulation of synapse organization / Recycling pathway of L1 / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / homeostasis of number of cells within a tissue / response to mechanical stimulus / sperm flagellum / adult locomotory behavior / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / condensed chromosome / Activation of AMPK downstream of NMDARs / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to calcium ion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / neuron migration / visual learning / cerebral cortex development / RHO GTPases Activate Formins / intracellular protein transport / memory / synapse organization / PKR-mediated signaling / microtubule cytoskeleton organization / recycling endosome / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / mitotic spindle / structural constituent of cytoskeleton / neuron differentiation / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / neuron apoptotic process / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / protein-folding chaperone binding / cilium / microtubule binding / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein stabilization / protein heterodimerization activity / cell division / hydrolase activity / GTPase activity / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome
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
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
Revision 1.1Apr 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2May 6, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2May 6, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more