[English] 日本語
Yorodumi
- EMDB-17391: Subtomogram average of ribosomes in germinated polar tubes of Vai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17391
TitleSubtomogram average of ribosomes in germinated polar tubes of Vairimorpha necatrix
Map datasubtomogram average of ribosome from Vairimorpha necatrix
Sample
  • Complex: Ribosome monomers from germinated polar tubes.
KeywordsRibosome / Subtomogram / Microsporidia
Biological speciesVairimorpha necatrix (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 46.0 Å
AuthorsSharma H / Ehrenbolger K / Jespersen N / Carlson LA / Barandun J
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)948655European Union
European Commission101033469European Union
CitationJournal: Biorxiv / Year: 2023
Title: Ribosome clustering and surface layer reorganization in the microsporidian host-invasion apparatus
Authors: Sharma H / Jespersen N / Ehrenbolger K / Carlson LA / Barandun J
History
DepositionMay 18, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17391.png

Downloads & links

-
Map

FileDownload / File: emd_17391.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of ribosome from Vairimorpha necatrix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.69 Å/pix.
x 64 pix.
= 556.16 Å		8.69 Å/pix.
x 64 pix.
= 556.16 Å		8.69 Å/pix.
x 64 pix.
= 556.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.1
Minimum - Maximum-18.054472000000001 - 9.901574999999999
Average (Standard dev.)-0.017061207 (±0.967578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 556.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17391_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 for ribosome subtomogram

Fileemd_17391_half_map_1.map
AnnotationHalf map 1 for ribosome subtomogram
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 for ribosome subtomogram

Fileemd_17391_half_map_2.map
AnnotationHalf map 2 for ribosome subtomogram
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ribosome monomers from germinated polar tubes.

EntireName: Ribosome monomers from germinated polar tubes.
Components
  • Complex: Ribosome monomers from germinated polar tubes.

-
Supramolecule #1: Ribosome monomers from germinated polar tubes.

SupramoleculeName: Ribosome monomers from germinated polar tubes. / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vairimorpha necatrix (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
1.0 mMC4H11NO3Tris-HClTris
0.17 mMKClPotassium Chloride
10.0 mMC10H16N2O8EDTAEthylenediaminetetraacetic acid

Details: Germination buffer (0.17 mM KCl, 1 mM Tris-HCl (pH 8.0), 10 mM EDTA)
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsGerminated polar tubes were stacked with ribosome arrays.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 25 / Number images used: 3000
Reference model: Generated by averaging manually picked particles
Software - Name: Dynamo (ver. 1.1.532)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 46.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 7000

+
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