[English] 日本語
Yorodumi
- EMDB-26209: Subtomogram average of central pair complex from Salpingoeca rose... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26209
TitleSubtomogram average of central pair complex from Salpingoeca rosetta (choanoflagellate)
Map dataSubtomogram average of Salpingoeca rosetta (choanoflagellate) ciliary central pair complex
Sample
  • Organelle or cellular component: central pair complex from Salpingoeca rosetta cilia
Keywordscilia microtubule central pair / STRUCTURAL PROTEIN
Biological speciesSalpingoeca rosetta (eukaryote)
Methodelectron tomography / cryo EM / Resolution: 25.0 Å
AuthorsPinskey JM / Nicastro D
Funding support United States, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM083122 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM137470 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR140082 United States
CitationJournal: Elife / Year: 2022
Title: Ciliary 96-nm repeat unit from Salpingoeca rosetta (choanoflagellate), generated via cryo-electron tomography and subtomogram averaging.
Authors: Pinskey JM / Nicastro D
History
DepositionFeb 15, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26209.png

Downloads & links

-
Map

FileDownload / File: emd_26209.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Salpingoeca rosetta (choanoflagellate) ciliary central pair complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.15 Å/pix.
x 300 pix.
= 945.3 Å		3.15 Å/pix.
x 300 pix.
= 945.3 Å		3.15 Å/pix.
x 300 pix.
= 945.3 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.151 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum121.299790000000002 - 137.8416
Average (Standard dev.)127.729004000000003 (±1.6702932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 945.3 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : central pair complex from Salpingoeca rosetta cilia

EntireName: central pair complex from Salpingoeca rosetta cilia
Components
  • Organelle or cellular component: central pair complex from Salpingoeca rosetta cilia

-
Supramolecule #1: central pair complex from Salpingoeca rosetta cilia

SupramoleculeName: central pair complex from Salpingoeca rosetta cilia / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: Contains microtubules and central pair projections
Source (natural)Organism: Salpingoeca rosetta (eukaryote) / Location in cell: cilium

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
Cryo protectantliquid ethane
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Millipore Sigma / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / 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