[English] 日本語
Yorodumi
- PDB-2noq: Structure of ribosome-bound cricket paralysis virus IRES RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2noq
TitleStructure of ribosome-bound cricket paralysis virus IRES RNA
Components
  • (18S ribosomal ...) x 3
  • (60S ribosomal protein ...) x 2
  • 25S ribosomal RNA
  • 40S ribosomal protein S5
  • CrPV IRESCripavirus internal ribosome entry site
KeywordsRIBOSOME / IRES RNA / Translation / Internal Initiation
Function / homology
Function and homology information


: / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...: / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / maturation of LSU-rRNA / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. ...Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL1A / Small ribosomal subunit protein uS7 / 60S ribosomal protein L1-B / Large ribosomal subunit protein uL5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsSchuler, M. / Connell, S.R. / Lescoute, A. / Giesebrecht, J. / Dabrowski, M. / Schroeer, B. / Mielke, T. / Penczek, P.A. / Westhof, E. / Spahn, C.M.T.
CitationJournal: Nat Struct Mol Biol / Year: 2006
Title: Structure of the ribosome-bound cricket paralysis virus IRES RNA.
Authors: Martin Schüler / Sean R Connell / Aurelie Lescoute / Jan Giesebrecht / Marylena Dabrowski / Birgit Schroeer / Thorsten Mielke / Pawel A Penczek / Eric Westhof / Christian M T Spahn /
Abstract: Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ...Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ribosomal complexes in the absence of canonical initiation factors and initiator transfer RNA. We present here a cryo-EM reconstruction of a dicistroviral IRES bound to the 80S ribosome. The resolution of the cryo-EM reconstruction, in the subnanometer range, allowed the molecular structure of the complete IRES in its active, ribosome-bound state to be solved. The structure, harboring three pseudoknot-containing domains, each with a specific functional role, shows how defined elements of the IRES emerge from a compactly folded core and interact with the key ribosomal components that form the A, P and E sites, where tRNAs normally bind. Our results exemplify the molecular strategy for recruitment of an IRES and reveal the dynamic features necessary for internal initiation.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1285
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1285
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CrPV IRES
B: 18S ribosomal RNA
C: 18S ribosomal RNA
D: 18S ribosomal RNA
E: 25S ribosomal RNA
F: 40S ribosomal protein S5
G: 60S ribosomal protein L1
H: 60S ribosomal protein L11-B


Theoretical massNumber of molelcules
Total (without water)161,1918
Polymers161,1918
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 2 types, 2 molecules AE

#1: RNA chain CrPV IRES / Cripavirus internal ribosome entry site


Mass: 60828.805 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This chain, CrPV-IRES-RNA [NCBI accession: BD177018], was synthesized by in-vitro transcription of a plasmid template
References: GenBank: 8895506
#5: RNA chain 25S ribosomal RNA / / S2 / YS8 / RP14


Mass: 17186.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
18S ribosomal ... , 3 types, 3 molecules BCD

#2: RNA chain 18S ribosomal RNA /


Mass: 14869.938 Da / Num. of mol.: 1 / Fragment: residues 500-545 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain 18S ribosomal RNA /


Mass: 4149.502 Da / Num. of mol.: 1 / Fragment: residues 1050-1062 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#4: RNA chain 18S ribosomal RNA /


Mass: 4784.873 Da / Num. of mol.: 1 / Fragment: residues 1194-1208 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

-
Protein , 1 types, 1 molecules F

#6: Protein 40S ribosomal protein S5 / / L10a


Mass: 16577.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783

-
60S ribosomal protein ... , 2 types, 2 molecules GH

#7: Protein 60S ribosomal protein L1 / / L16 / YL16 / 39B / RP39


Mass: 24014.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53030, UniProt: P0CX43*PLUS
#8: Protein 60S ribosomal protein L11-B / Ribosome


Mass: 18780.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E757

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Yeast 80S bound by cricket paralysis virus IRES RNA / Type: VIRUS
Buffer solutionName: 20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor
pH: 7.6
Details: 20 mM Hepes pH 7.6, 100 mM KAc, 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1mM AEBSF, Roche Complete Protease Inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
DetectorType: KODAK SO163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Iterative 3D-Projection Matching / Resolution: 7.3 Å / Num. of particles: 73313 / Nominal pixel size: 1.22 Å / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11S1I

1s1i
PDB Unreleased entry

11S1I1PDBexperimental model
21S1H

1s1h
PDB Unreleased entry

11S1H2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4163 6746 0 0 10909

+
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