[English] 日本語
Yorodumi
- EMDB-17908: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17908
TitleChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
Map dataChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D - local resolution filtered
Sample
  • Complex: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
Keywordsbiogenesis / pre-60S / 5S RNP / RIBOSOME
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsThoms M / Cheng J / Denk T / Berninghausen O / Beckmann R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO Rep / Year: 2023
Title: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Authors: Matthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from ...The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.
History
DepositionJul 15, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17908.png

Downloads & links

-
Map

FileDownload / File: emd_17908.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D - local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å		1.05 Å/pix.
x 500 pix.
= 522.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.970281 - 8.546847
Average (Standard dev.)0.0025896993 (±0.08029772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 522.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation...

Fileemd_17908_additional_1.map
AnnotationChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation...

Fileemd_17908_half_map_1.map
AnnotationChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D - half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation...

Fileemd_17908_half_map_2.map
AnnotationChaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 in...

EntireName: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
Components
  • Complex: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D

-
Supramolecule #1: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 in...

SupramoleculeName: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#64
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74642
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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