[English] 日本語
Yorodumi
- PDB-2ap5: Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudokn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ap5
TitleSolution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, Average Structure
ComponentsC27A Sugarcane Yellow Leaf Virus RNA pseudoknot
KeywordsRNA / RNA pseudoknot / frameshifting
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing starting with random coordinates, refinement with residual dipolar couplings
Model type detailsminimized average
AuthorsCornish, P.V. / Giedroc, D.P.
CitationJournal: Rna / Year: 2006
Title: The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical
Authors: Cornish, P.V. / Stammler, S.N. / Giedroc, D.P.
History
DepositionAug 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C27A Sugarcane Yellow Leaf Virus RNA pseudoknot


Theoretical massNumber of molelcules
Total (without water)9,0251
Polymers9,0251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

-
Components

#1: RNA chain C27A Sugarcane Yellow Leaf Virus RNA pseudoknot


Mass: 9024.501 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Mutant of naturally occuring RNA fragment that forms an RNA pseudoknot in Sugarcane Yellow Leaf Virus

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
243TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.7mM C27A ScYLV, 100mM KCl, 5mM MgCl290% H2O/10% D2O
22.7mM C27A ScYLV, 100mM KCl, 5mM MgCl2100% D2O
32.7mM C27A ScYLV, 100mM KCl, 5mM MgCl2, 15 mg/ml PF1 phage100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM KCl, 5mM MgCl2 6ambient 283 K
2100mM KCl, 5mM MgCl2 6ambient 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeMac OS X versionF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
Sparky3T. D. Goddard and D. G. Knellerdata analysis
XPLOR-NIH2.1G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandrastructure solution
XPLOR-NIH2.1G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
RefinementMethod: simulated annealing starting with random coordinates, refinement with residual dipolar couplings
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

+
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