[English] 日本語
Yorodumi
- PDB-2ky2: The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ky2
TitleThe Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU
Components5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3'
KeywordsRNA / tandem AG pairs / thermodynamics / imino AG pair / dual syn GG pair / extrahelical U
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsHammond, N.B. / Kennedy, S.D. / Turner, D.H.
CitationJournal: Biochemistry / Year: 2010
Title: RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.
Authors: Hammond, N.B. / Tolbert, B.S. / Kierzek, R. / Turner, D.H. / Kennedy, S.D.
History
DepositionMay 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,8222
Polymers5,8222
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)10 / 40structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

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


Mass: 2910.807 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Tandem AG pairs with UG closing pairs: r(GGUAGGCCA)2
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-13C HSQC
1322D 1H-1H TOCSY
1422D DQF-COSY
1522D 1H-31P HETCOR
1622D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-11
80 mMsodium chloride-21
10 mMsodium phosphate-31
0.5 mMEDTA-41
1 mMRNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-52
80 mMsodium chloride-62
10 mMsodium phosphate-72
0.5 mMEDTA-82
Sample conditionsIonic strength: 0.1 / pH: 6.1 / Pressure: ambient / Temperature: 274 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
Sparky3.12Goddardchemical shift assignment
Sparky3.12Goddarddata analysis
VNMR6.1CVariancollection
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 10

+
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