[English] 日本語
Yorodumi
- PDB-2ke6: Solution Structure of K10 TLS RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ke6
TitleSolution Structure of K10 TLS RNA
ComponentsK10 TLS RNA
KeywordsRNA / RNA transport / RNA hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing, restrained molecular dynamics with RDCs
Model detailslowest energy, model 1
AuthorsBullock, S.L. / Ringel, I. / Ish-Horowicz, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A'-form RNA helices are required for cytoplasmic mRNA transport in Drosophila
Authors: Bullock, S.L. / Ringel, I. / Ish-Horowicz, D. / Lukavsky, P.J.
History
DepositionJan 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K10 TLS RNA


Theoretical massNumber of molelcules
Total (without water)15,2551
Polymers15,2551
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)12 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain K10 TLS RNA


Mass: 15255.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PREPARED BY IN VITRO TRANSCRIPTION USING T7 / Source: (synth.) Drosophila melanogaster (fruit fly)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D 1H-1H TOCSY
1422D DQF-COSY
1522D HP COSY
1632D 1H-1H NOESY
1742D 1H-1H NOESY
1852D HNN COSY
1963D (H)CCH-TOCSY
11063D (H)CCH-COSY
11163D 13C NOESY-HSQC
11263D HCP
11363D 13C HMQC TOCSY
11462D 13C CT-TROSY
NMR detailsText: STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE, MULTIDIMENSIONAL NMR SPECTROSCOPY AND TROSY-TYPE EXPERIMENTS TO MEASURE RESIDUAL DIPOLAR COUPLINGS

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM K10 RNA; 95% H2O/5% D2O95% H2O/5% D2O
21.0mM K10 RNA; 100% D2O100% D2O
31.0mM K10 RNA; 95% H2O/5% D2O95% H2O/5% D2O
41.0mM K10 RNA; 100% D2O100% D2O
50.8mM [U-99% 13C; U-99% 15N] K10 RNA; 5% D2O95% H2O/5% D2O
60.8mM [U-99% 13C; U-99% 15N] K10 RNA; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMK10 RNA-1natural abundance1
1.0 mMK10 RNA-2pyrimidine H5-deuterated2
0.8 mMK10 RNA-3[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 0.01 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, restrained molecular dynamics with RDCs
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 12 / Representative conformer: 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