[English] 日本語
Yorodumi
- PDB-1q8n: Solution Structure of the Malachite Green RNA Binding Aptamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q8n
TitleSolution Structure of the Malachite Green RNA Binding Aptamer
ComponentsRNA Aptamer
KeywordsRNA / rna aptamer / malachite green / base triple / base quadruple / rna ligand interactions
Function / homologyMALACHITE GREEN / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFlinders, J. / DeFina, S.C. / Brackett, D.M. / Baugh, C. / Wilson, C. / Dieckmann, T.
CitationJournal: Chembiochem / Year: 2004
Title: Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex.
Authors: Flinders, J. / DeFina, S.C. / Brackett, D.M. / Baugh, C. / Wilson, C. / Dieckmann, T.
History
DepositionAug 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA Aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6472
Polymers12,3171
Non-polymers3291
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA Aptamer


Mass: 12317.421 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was synthesized in vitro and does not occur naturally.
#2: Chemical ChemComp-MGR / MALACHITE GREEN


Mass: 329.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N2 / Comment: Antimicrobial*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
2222D TOCSY
232DQF-COSY
2443D 13C-separated NOESY
1552D HMQC
264HCNCH
1732D NOESY
NMR detailsText: This structure was determined with the aid of the crystal structure of a similar RNA aptamer.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM RNA Aptamer, 10mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM RNA Aptamer, 10mM phosphate buffer, 100% D2O100% D2O
31.5mM RNA Aptamer, 10mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
41mM RNA Aptamer U-15N,13C, 10mM phosphate buffer, 100% D2O100% D2O
51mM RNA Aptamer U-15N,13C, 10mM phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM KCl 5.8ambient 274 K
210mM KCl 5.8ambient 298 K
310mM KCl 5.8ambient 274 K
410mM KCl 5.8ambient 298 K
510mM KCl 5.8ambient 274 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
CNS1.1A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warrenstructure solution
XEASY1.3.13C. Bartels, T.H. Xia, M. Billeter, P. Gntert and K. Wthrichdata analysis
CNS1.1A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M.R ice, T. Simonson, G.L. Warrenrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was based on 423 NOE constraints (148 intranucleotide, 119 sequential, 66 medium to long range, and 90 RNA to ligand NOEs) and 219 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

+
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