[English] 日本語
Yorodumi
- EMDB-15249: Microtubules -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15249
TitleMicrotubules
Map data
Sample
  • Complex: Microtubules
Biological speciesSus scrofa (pig)
Methodelectron tomography / cryo EM
AuthorsVolkov VA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: J Cell Biol / Year: 2023
Title: CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side.
Authors: Cyntha M van den Berg / Vladimir A Volkov / Sebastian Schnorrenberg / Ziqiang Huang / Kelly E Stecker / Ilya Grigoriev / Sania Gilani / Kari-Anne M Frikstad / Sebastian Patzke / Timo ...Authors: Cyntha M van den Berg / Vladimir A Volkov / Sebastian Schnorrenberg / Ziqiang Huang / Kelly E Stecker / Ilya Grigoriev / Sania Gilani / Kari-Anne M Frikstad / Sebastian Patzke / Timo Zimmermann / Marileen Dogterom / Anna Akhmanova /
Abstract: Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling the formation of ...Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling the formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates the elongation and stability of ciliary axonemes and other microtubule-based structures.
#1: Journal: Biorxiv / Year: 2022
Title: CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side
Authors: van den Berg CM / Volkov VA / Schnorrenberg S / Huang Z / Stecker KE / Grigoriev I / Patzke S / Zimmermann T / Dogterom M / Akhmanova A
History
DepositionJun 24, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15249.png

Downloads & links

-
Map

FileDownload / File: emd_15249.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 252 pix.
= 184.968 Å		0.73 Å/pix.
x 1920 pix.
= 1409.28 Å		0.73 Å/pix.
x 1856 pix.
= 1362.304 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: 0.734 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-727.47 - 544.87933
Average (Standard dev.)1.8667017 (±37.04449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-325315-1259
Dimensions19201856252
Spacing18561920252
CellA: 1362.3041 Å / B: 1409.28 Å / C: 184.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Microtubules

EntireName: Microtubules
Components
  • Complex: Microtubules

-
Supramolecule #1: Microtubules

SupramoleculeName: Microtubules / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

-
Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma / Diameter: 5 nm

-
Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 10000

-
Image processing

Final reconstructionNumber 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