[English] 日本語
Yorodumi
- EMDB-3558: Centriolar Proximal MT triplet in centrosomes extracted from o.ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3558
TitleCentriolar Proximal MT triplet in centrosomes extracted from o.aries thymocytes
Map dataCentriolar proximal MT triplet from a mammal centrosome. Centrosomes were extracted from o.aries thymocytes.
Sample
  • Organelle or cellular component: Centrosome enriched from young lamb thymocytes
Biological speciesOvis aries (sheep)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsBusselez J / Chichon FJ / Melero R / Carrascosa JL / Carazo JM
CitationJournal: Sci Rep / Year: 2019
Title: Cryo-Electron Tomography and Proteomics studies of centrosomes from differentiated quiescent thymocytes.
Authors: Johan Busselez / Francisco Javier Chichón / Maria Josefa Rodríguez / Adan Alpízar / Séverine Isabelle Gharbi / Mònica Franch / Roberto Melero / Alberto Paradela / José L Carrascosa / José-Maria Carazo /
Abstract: We have used cryo Electron Tomography, proteomics and immunolabeling to study centrosomes isolated from the young lamb thymus, an efficient source of quiescent differentiated cells. We compared the ...We have used cryo Electron Tomography, proteomics and immunolabeling to study centrosomes isolated from the young lamb thymus, an efficient source of quiescent differentiated cells. We compared the proteome of thymocyte centrosomes to data published for KE37 cells, focusing on proteins associated with centriole disengagement and centrosome separation. The data obtained enhances our understanding of the protein system joining the centrioles, a system comprised of a branched network of fibers linked to an apparently amorphous density that was partially characterized here. A number of proteins were localized to the amorphous density by immunolabeling (C-NAP1, cohesin SMC1, condensin SMC4 and NCAPD2), yet not DNA. In conjuction, these data not only extend our understanding of centrosomes but they will help refine the model that focus on the protein system associated with the centriolar junction.
History
DepositionDec 24, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseAug 22, 2018-
UpdateAug 22, 2018-
Current statusAug 22, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3558.png

Downloads & links

-
Map

FileDownload / File: emd_3558.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCentriolar proximal MT triplet from a mammal centrosome. Centrosomes were extracted from o.aries thymocytes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 300 pix.
= 1026. Å		3.42 Å/pix.
x 300 pix.
= 1026. Å		3.42 Å/pix.
x 300 pix.
= 1026. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-5.3274627 - 7.500101
Average (Standard dev.)0.047066804 (±0.48473692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 1026.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z1026.0001026.0001026.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-5.3277.5000.047

-
Supplemental data

-
Sample components

-
Entire : Centrosome enriched from young lamb thymocytes

EntireName: Centrosome enriched from young lamb thymocytes
Components
  • Organelle or cellular component: Centrosome enriched from young lamb thymocytes

-
Supramolecule #1: Centrosome enriched from young lamb thymocytes

SupramoleculeName: Centrosome enriched from young lamb thymocytes / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: The centrosome were extracted accordingly to Komesli et al. 1989
Source (natural)Organism: Ovis aries (sheep) / Organ: Thymus / Tissue: Thymus Lobules / Organelle: Centrosome / Location in cell: cytoplasm near the nucleus
Molecular weightExperimental: 230000 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

Concentration0.076 mg/mL
BufferpH: 7.2 / Component - Concentration: 10.0 mM / Component - Formula: C8H18N2O6S2 / Component - Name: Pipes / Details: pH rectification with KOH
GridModel: quantifoil 3.5/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
DetailsThe sample was enriched by two step of sedimentation in sucrose gradient. The sucrose was washed out in several drops of buffer, the last of which included fiducial markers (10 nm bovine serum albumin (BSA)-coated gold beads) for tilt series alignment

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Gatan 968 Quantum / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 1.0 sec. / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.906 µm / Calibrated defocus min: 5.54 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 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

DetailsTilt series were aligned based on fiducials with IMOD and mass normalized using PRIISM. The ctf correction was processed on tilt series using TomoCTF. Tomogram were reconstructed using SIRT algorithm with TOMO3D. The number of frames per image were variable, with 8 frames at full tilt, through to 4 frames at zero tilt.
Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Dynamo (ver. 1.1.22) / Number subtomograms used: 282
ExtractionNumber tomograms: 4 / Number images used: 800 / Method: volume picked interactively / Software - Name: Dynamo (ver. 1.1.22)
Details: Coarse models of the centriole microtubules were obtained using Fiber Tracing in Amira and converted for import in dynamo. From those coarse models, "filament with torsion" models were ...Details: Coarse models of the centriole microtubules were obtained using Fiber Tracing in Amira and converted for import in dynamo. From those coarse models, "filament with torsion" models were traced in dynamo. The triplets were segregated from the doublets and triplets volume particle were windowed with overlap every 8.3nm along the "filament with torsion" models
CTF correctionSoftware - Name: TOMOCTF / Details: wiener filtering, made on tilt series
Final 3D classificationNumber classes: 4 / Software - Name: Dynamo (ver. 1.1.22) / Details: classification by PCA + k-means
Final angle assignmentType: OTHER / Software - Name: Dynamo (ver. 1.1.22)
Details: The particular geometry of the centriole with its repeat every 8.3nm along the proximal-distal axis and its coarse 9 fold symmetry was used to construct from each tomogram a model lowly ...Details: The particular geometry of the centriole with its repeat every 8.3nm along the proximal-distal axis and its coarse 9 fold symmetry was used to construct from each tomogram a model lowly affected by missing wedge. Those coarse models were volume aligned and an initial reference were averaged from all the subtomogram particle using the coarse orientation of the particles determined that way. This model was iteratively refined. The reference model for the next iteration was made using 70% of the particles based on the best correlation during the alignment. For the finer step of refinement, a mask was used to restrict the alignment to an area covering 3 of the 8.3nm repeats.
Crystal parametersUnit cell - A: 1026 Å / Unit cell - B: 1026 Å / Unit cell - C: 249.66 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P1
FSC plot (resolution estimation)

+
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