[English] 日本語
Yorodumi
- EMDB-15443: In situ cryo-electron tomogram of a Taxol treated intact pluripot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15443
TitleIn situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
Map dataIn situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
Sample
  • Cell: In situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
KeywordsMicrotubules / Scaffold / protein transport
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsChakraborty S / Martinez-Sanchez A / Baumeister W / Mahamid J
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other government Germany
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-ET suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules.
Authors: Saikat Chakraborty / Antonio Martinez-Sanchez / Florian Beck / Mauricio Toro-Nahuelpan / In-Young Hwang / Kyung-Min Noh / Wolfgang Baumeister / Julia Mahamid /
Abstract: The functional architecture of the long-lived neuronal microtubule (MT) cytoskeleton is maintained by various MT-associated proteins (MAPs), most of which are known to bind to the MT outer surface. ...The functional architecture of the long-lived neuronal microtubule (MT) cytoskeleton is maintained by various MT-associated proteins (MAPs), most of which are known to bind to the MT outer surface. However, electron microscopy (EM) has long ago revealed the presence of particles inside the lumens of neuronal MTs, of yet unknown identity and function. Here, we use cryogenic electron tomography (cryo-ET) to analyze the three-dimensional (3D) organization and structures of MT lumenal particles in primary hippocampal neurons, human induced pluripotent stem cell-derived neurons, and pluripotent and differentiated P19 cells. We obtain in situ density maps of several lumenal particles from the respective cells and detect common structural features underscoring their potential overarching functions. Mass spectrometry-based proteomics combined with structural modeling suggest that a subset of lumenal particles could be tubulin-binding cofactors (TBCs) bound to tubulin monomers. A different subset of smaller particles, which remains unidentified, exhibits densities that bridge across the MT protofilaments. We show that increased lumenal particle concentration within MTs is concomitant with neuronal differentiation and correlates with higher MT curvatures. Enrichment of lumenal particles around MT lattice defects and at freshly polymerized MT open-ends suggests a MT protective role. Together with the identified structural resemblance of a subset of particles to TBCs, these results hint at a role in local tubulin proteostasis for the maintenance of long-lived neuronal MTs.
#1: Journal: Biorxiv / Year: 2024
Title: Cryo-electron tomography suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules
Authors: Chakraborty S / Martinez-Sanchez A / Beck F / Toro-Nahuelpan M / Hwang IY / Noh KM / Baumeister W / Mahamid J
History
DepositionJul 21, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15443.png

Downloads & links

-
Map

FileDownload / File: emd_15443.map.gz / Format: CCP4 / Size: 102.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationIn situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
27.36 Å/pix.
x 250 pix.
= 6840. Å		27.36 Å/pix.
x 464 pix.
= 12695.04 Å		27.36 Å/pix.
x 464 pix.
= 12695.04 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 27.36 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-96.0 - 75.0
Average (Standard dev.)2.6191928 (±5.3814154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-125
Dimensions464464250
Spacing464464250
CellA: 12695.04 Å / B: 12695.04 Å / C: 6840.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : In situ cryo-electron tomogram of a Taxol treated intact pluripot...

EntireName: In situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
Components
  • Cell: In situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.

-
Supramolecule #1: In situ cryo-electron tomogram of a Taxol treated intact pluripot...

SupramoleculeName: In situ cryo-electron tomogram of a Taxol treated intact pluripotent P19 cell.
type: cell / ID: 1 / Parent: 0
Details: The cells were treated with Taxol for 30 minutes prior to vitrification
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV
Details: blot force 10, blot time 10 seconds from backside..
DetailsCells are cultured on EM grid
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 42000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9.0) / Number images used: 61

+
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