[English] 日本語
Yorodumi
- PDB-2l8u: NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l8u
TitleNMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1 - UU pair with one hydrogen bond pair
ComponentsRNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')
KeywordsRNA / UU mismatch
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 1
AuthorsParkesh, R. / Fountain, M.A. / Disney, M.D.
CitationJournal: Biochemistry / Year: 2011
Title: NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)(2) Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
Authors: Parkesh, R. / Fountain, M. / Disney, M.D.
History
DepositionJan 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2023Group: Data collection / Database references / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')
B: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,7262
Polymers5,7262
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 / 25structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

-
Components

#1: RNA chain RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')


Mass: 2862.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: duplex with UU Internal Loop Found in Myotonic Dystrophy Type 1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

-
Sample preparation

DetailsContents: 1.5 mM RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3'), 100% D2O
Solvent system: 100% D2O
SampleConc.: 1.5 mM / Component: RNA (5'-R(*CP*CP*GP*CP*UP*GP*CP*GP*G)-3')-1
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 313 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddarddata analysis
Sparky3.111Goddardpeak picking
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 25 / Conformers 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