[English] 日本語
Yorodumi
- EMDB-24283: Exon-free state of the Tetrahymena group I intron, symmetry-expan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24283
TitleExon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
Map dataExon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
Sample
  • Complex: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
    • RNA: Group I intronGroup I catalytic intron
  • Ligand: MAGNESIUM ION
KeywordsRibozyme / catalytic RNA / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsThelot F / Liu D
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122797 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5DP1GM133052 United States
National Science Foundation (NSF, United States)CMMI-1333215 United States
National Science Foundation (NSF, United States)CMMI-1344915 United States
National Science Foundation (NSF, United States)CBET-1729397 United States
CitationJournal: Nat Methods / Year: 2022
Title: Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly.
Authors: Di Liu / François A Thélot / Joseph A Piccirilli / Maofu Liao / Peng Yin /
Abstract: High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural ...High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy-ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops)-involves installing kissing-loop sequences onto the functionally nonessential stems of RNAs for homomeric self-assembly into closed rings with multiplied molecular weights and mitigated structural flexibility. ROCK enables cryo-EM reconstruction of the Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA, including the previously unknown peripheral domains. ROCK is further applied to two smaller RNAs-the Azoarcus group I intron and the FMN riboswitch, revealing the conformational change of the former and the bound ligand in the latter. ROCK holds promise to greatly facilitate the use of cryo-EM in RNA structural studies.
History
DepositionJun 22, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_24283.png

Downloads & links

-
Map

FileDownload / File: emd_24283.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-1.9306813 - 2.6865819
Average (Standard dev.)0.000000000003653 (±0.20125549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin1367592
Dimensions818096
Spacing968180
CellA: 119.04 Å / B: 100.44 Å / C: 99.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Exon-free state of Tetrahymena group I intron, symmetry-expanded ...

EntireName: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
Components
  • Complex: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
    • RNA: Group I intronGroup I catalytic intron
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Exon-free state of Tetrahymena group I intron, symmetry-expanded ...

SupramoleculeName: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Synthetically produced: Yes
Molecular weightTheoretical: 130 KDa

-
Macromolecule #1: Group I intron

MacromoleculeName: Group I intron / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 127.005961 KDa
SequenceString: UGGAGGGAAA AGUUAUCAGG CAUGCACCUG GUAGCUAGUC UUUAAACCAA UAGAUUGCAU CGGUUUAAAA GGCAAGACCG UCAAAUUGC GGGAAAGGGG UCAACAGCCG UUCAGUACCA AGUCUCAGGG GAAACUUUGA GAUGGCCUUG CAAAGGGUAU G GUAAUAAG ...String:
UGGAGGGAAA AGUUAUCAGG CAUGCACCUG GUAGCUAGUC UUUAAACCAA UAGAUUGCAU CGGUUUAAAA GGCAAGACCG UCAAAUUGC GGGAAAGGGG UCAACAGCCG UUCAGUACCA AGUCUCAGGG GAAACUUUGA GAUGGCCUUG CAAAGGGUAU G GUAAUAAG CUGACGGACA UGGUCCUAAC CACGCAGCCA AGUCCUAAGU CAACAGGAUG GUUCUGUUGA UAUGGAUGCA GU UCACAGA CUAAAUGUCG GUCGGGGAAG AUGUAUUCUU CUCAUAAGAU AUAGUCGGAC CUCUCCUUAA UGGGAGCUAG CGG AUGAAG UGAUGCAACA CUGGAGCCGC UGGGAACUAA UCAGUGAACC AUCCACUGAU UAGUUUUGGA GUACUCG

GENBANK: GENBANK: V01416.1

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-acetateTris-acetate
30.0 mMMgCl2Magnesium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85596

+
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