[English] 日本語
Yorodumi
- PDB-2k66: NMR solution structure of the d3'-stem closed by a GAAA tetraloop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k66
TitleNMR solution structure of the d3'-stem closed by a GAAA tetraloop of the group II intron Sc.ai5(gamma)
Components5'-R(*GP*GP*AP*GP*UP*AP*UP*GP*UP*GP*AP*AP*AP*GP*CP*AP*UP*AP*CP*UP*CP*C)-3'
KeywordsRNA / group II intron / ribozyme / splicing / d3'-stem / GAAA tetraloop / RNA 22-mer / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKruschel, D. / Sigel, R.K.O.
CitationJournal: Rna / Year: 2014
Title: NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Authors: Kruschel, D. / Skilandat, M. / Sigel, R.K.
History
DepositionJul 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 12, 2014Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,0821
Polymers7,0821
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 7082.274 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H NOESY
1312D 1H-1H TOCSY
2412D 1H-1H TOCSY
3522D 1H-1H NOESY
4622D 1H-1H NOESY
5732D 1H-13C HSQC
6842D 1H-15N HSQC
7942D JNN HNN-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
41.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMRNA (22-MER)1
10 mMpotassium chloride1
10 uMEDTA1
0.9 mMRNA (22-MER)2
10 mMpotassium chloride2
10 uMEDTA2
1.0 mMRNA (22-MER)[U-100% 13C; U-100% 15N]3
10 mMpotassium chloride3
10 uMEDTA3
1.0 mMRNA (22-MER)[U-100% 13C; U-100% 15N]4
10 mMpotassium chloride4
10 uMEDTA4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1106.0-6.1 ambient 293 K
2106.0-6.1 ambient 303 K
3106.2ambient 278 K
4106.2ambient 293 K
5106.4ambient 303 K
6106.4ambient 278 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 471 / NOE intraresidue total count: 157 / NOE long range total count: 86 / NOE medium range total count: 0 / NOE sequential total count: 228
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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