[English] 日本語
Yorodumi
- PDB-2l1v: Solution structure of a preQ1 riboswitch (Class I) aptamer bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l1v
TitleSolution structure of a preQ1 riboswitch (Class I) aptamer bound to preQ1
Components36-MER
KeywordsRNA / preQ1 / riboswitch / aptamer / pseudoknot
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKang, M. / Zhang, Q. / Feigon, J.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA
Authors: Kang, M. / Peterson, R.D. / Feigon, J.
History
DepositionAug 6, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
SupersessionJan 19, 2011ID: 2KFC
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: 36-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7072
Polymers11,5281
Non-polymers1791
Water0
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 36-MER


Mass: 11527.904 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1413D (H)CCH-TOCSY
1512D DQF-COSY
1612D 1H-13C HSQC
1722D 1H-15N COSY
1832D 1H-13C HSQC
1932D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM preQ1-RNA 36mer, 1 mM [U-13C; U-15N]-Cyt preQ1-RNA 36mer, 1 mM [U-13C; U-15N]-Ade preQ1-RNA 36mer, 1 mM [U-13C; U-15N]-Gua preQ1-RNA 36mer, 1 mM [U-13C; U-15N]-Ura preQ1-RNA 36mer, 1 mM U-H5,3',4',5',5''-2H preQ1-RNA 36mer, 100% D2O100% D2O
21 mM preQ1-RNA 36mer, 1 mM [U-13C; U-15N] preQ1-RNA 36mer, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-13C; U-15N] preQ1-RNA 36mer, 90% H2O/10% D2O, phage90% H2O/10% D2O, phage
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpreQ1-RNA 36mer-11
1 mMpreQ1-RNA 36mer-2[U-13C; U-15N]-Cyt1
1 mMpreQ1-RNA 36mer-3[U-13C; U-15N]-Ade1
1 mMpreQ1-RNA 36mer-4[U-13C; U-15N]-Gua1
1 mMpreQ1-RNA 36mer-5[U-13C; U-15N]-Ura1
1 mMpreQ1-RNA 36mer-6U-H5,3',4',5',5''-2H1
1 mMpreQ1-RNA 36mer-72
1 mMpreQ1-RNA 36mer-8[U-13C; U-15N]2
0.7 mMpreQ1-RNA 36mer-9[U-13C; U-15N]3
Sample conditionsIonic strength: 50 / pH: 6.3 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

-
Processing

NMR software
NameDeveloperClassification
XwinNMRVariancollection
XwinNMRVarianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / 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: 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