[English] 日本語
Yorodumi
- PDB-12rt: In situ cryo-EM structure of axonal microtubules from ghost neuro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 12rt
TitleIn situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice)
Components
  • Detyrosinated tubulin alpha-1A chain
  • Tubulin beta-3 chain
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / microtubules / neuron / axon
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / netrin-activated signaling pathway / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / netrin receptor binding / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / pyramidal neuron differentiation ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / netrin-activated signaling pathway / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / netrin receptor binding / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / pyramidal neuron differentiation / COPI-mediated anterograde transport / Kinesins / PKR-mediated signaling / Aggrephagy / RHO GTPases activate IQGAPs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / glial cell differentiation / Resolution of Sister Chromatid Cohesion / dorsal root ganglion development / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / dentate gyrus development / axonemal microtubule / organelle transport along microtubule / Hedgehog 'off' state / RHO GTPases Activate Formins / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / forebrain morphogenesis / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / cerebellar cortex morphogenesis / Regulation of PLK1 Activity at G2/M Transition / MHC class II antigen presentation / neuron projection arborization / smoothened signaling pathway / homeostasis of number of cells within a tissue / motor behavior / adult behavior / response to L-glutamate / centrosome cycle / sperm principal piece / startle response / 'de novo' protein folding / intercellular bridge / flagellated sperm motility / regulation of synapse organization / sperm end piece / locomotory exploration behavior / microtubule polymerization / ciliary tip / response to tumor necrosis factor / response to mechanical stimulus / neuron apoptotic process / neurogenesis / sperm flagellum / adult locomotory behavior / cytoplasmic microtubule / condensed chromosome / peptide binding / cellular response to calcium ion / gene expression / visual learning / axon guidance / locomotory behavior / hippocampus development / cell periphery / filopodium / neuromuscular junction / myelin sheath / neuron migration / memory / cerebral cortex development / intracellular protein transport / synapse organization / microtubule cytoskeleton organization / recycling endosome / mitotic spindle / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / cilium / neuron differentiation / mitotic cell cycle / lamellipodium / growth cone / protein-folding chaperone binding / microtubule binding / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein stabilization / membrane raft / protein heterodimerization activity / protein domain specific binding / axon
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-3 chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsBodakuntla, S. / Marelli, J. / Vasquez-Montes, V. / 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: To Be Published
Title: Ghost neuron unlocks in situ high-resolution structural mapping of intracellular architecture in neurons
Authors: Bodakuntla, S. / Marelli, J. / Vasquez-Montes, V. / Biertumpfel, C. / Mizuno, N.
History
DepositionApr 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)203,34212
Polymers201,3124
Non-polymers2,0308
Water00
1


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

-
Components

#1: 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 / Strain: CD-1 / Tissue: Thalamus / References: UniProt: P68369
#2: 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 / Strain: CD-1 / Tissue: Thalamus / References: UniProt: Q9ERD7
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: 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
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Microtubule, axonal / Type: ORGANELLE OR CELLULAR COMPONENT
Details: explant axon from thalamus primary mouse embryo E15.5 tissue after ghost preparation (hypotonic treatment and mechanical plasma membrane removal)
Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD-1 / Cellular location: Axon / Organ: Brain / Tissue: Thalamus
Buffer solutionpH: 7.2 / Details: Gibco Neurobasal Media (diluted 1:3 to 160 mOsm)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: ghost neurons prepared by hypotonic and mechanical treatment
Specimen supportDetails: coated with poly-L-lysine and laminin / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K / Details: blot force 4, blot time 4 s

-
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: 3000 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: 52.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 10 / Num. of real images: 4172 / Details: curated image number
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 11520 / Height: 8184

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2SerialEMimage acquisition
4cryoSPARC4.7CTF correction
7UCSF ChimeraX1.9model fitting
8Coot0.9.8.93model fitting
10cryoSPARC4.7initial Euler assignment
11FREALIGN9.11final Euler assignment
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
14PHENIX2.0-5936model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 83.11 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 158108
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30423 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: iterative rounds of manual building and automated real-space refinement
Atomic model buildingPDB-ID: 9PND

9pnd


Accession code: 9PND / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00614036
ELECTRON MICROSCOPYf_angle_d0.73619036
ELECTRON MICROSCOPYf_dihedral_angle_d10.2861955
ELECTRON MICROSCOPYf_chiral_restr0.0472080
ELECTRON MICROSCOPYf_plane_restr0.0052478

+
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