[English] 日本語
Yorodumi
- EMDB-4934: Cryo-EM structure of the microsporidian ribosome: State 1, Multib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4934
TitleCryo-EM structure of the microsporidian ribosome: State 1, Multibody-refined map body 3 (SSU-head)
Map dataCryo-EM structure of the microsporidian ribosome: State 1, Multibody-refined map body 3 (SSU-head)
Sample
  • Complex: Microsporidian Ribosome
Biological speciesVairimorpha necatrix (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBarandun J / Hunziker M / Vossbrinck CR / Klinge S
Funding support United States, Switzerland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
CitationJournal: Nat Microbiol / Year: 2019
Title: Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.
Authors: Jonas Barandun / Mirjam Hunziker / Charles R Vossbrinck / Sebastian Klinge /
Abstract: Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are ...Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle, rudimentary mitochondria and the smallest known eukaryotic genomes. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.
History
DepositionMay 5, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseJul 10, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0133
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4934.png

Downloads & links

-
Map

FileDownload / File: emd_4934.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the microsporidian ribosome: State 1, Multibody-refined map body 3 (SSU-head)
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.0133 / Movie #1: 0.0133
Minimum - Maximum-0.037417214 - 0.0789112
Average (Standard dev.)0.00020532598 (±0.0028955368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 408.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0370.0790.000

-
Supplemental data

-
Sample components

-
Entire : Microsporidian Ribosome

EntireName: Microsporidian Ribosome
Components
  • Complex: Microsporidian Ribosome

-
Supramolecule #1: Microsporidian Ribosome

SupramoleculeName: Microsporidian Ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#78
Source (natural)Organism: Vairimorpha necatrix (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration11 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
30.0 mMTris-HCLTris
5.0 mMMgOAc
25.0 mMKCl
1.0 mMDTT
1.0 mMEDTAEthylenediaminetetraacetic acid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 3284 / Average exposure time: 0.25 sec. / Average electron dose: 5.55 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 471121
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC generated initial model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 185445
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4v88

RefinementProtocol: OTHER

+
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