[English] 日本語
Yorodumi
- PDB-2rn1: Liquid crystal solution structure of the kissing complex formed b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rn1
TitleLiquid crystal solution structure of the kissing complex formed by the apical loop of the HIV TAR RNA and a high affinity RNA aptamer optimized by SELEX
Components
  • RNA (5'-R(P*GP*AP*GP*CP*CP*CP*UP*GP*GP*GP*AP*GP*GP*CP*UP*C)-3')
  • RNA (5'-R(P*GP*CP*UP*GP*GP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3')
KeywordsRNA / RNA kissing complex / HIV TAR / High affinity RNA aptamer selected by SELEX / Liquid crystal NMR / GA base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsVan Melckebeke, H. / Devany, M. / Di Primo, C. / Beaurain, F. / Toulme, J. / Bryce, D.L. / Boisbouvier, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex
Authors: Van Melckebeke, H. / Devany, M. / Di Primo, C. / Beaurain, F. / Bryce, D.L. / Boisbouvier, J.
History
DepositionDec 5, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,2802
Polymers10,2802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 800structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 5168.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis
#2: RNA chain RNA (5'-R(P*GP*CP*UP*GP*GP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3') / TAR*GA


Mass: 5112.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-1H NOESY
1212D 1H-1H NOESY
1373D 1H-13C TROSY NOESY
3432D JNN-COSY
1573D (H)CCH-COSY
1683D (H)CCH-COSY
1773D HCN
1883D HCN
1972D intra base TOCSY
11083D 1H-13C TROSY NOESY
11182D intra base TOCSY
112813C-1H spin state selective experiments
113713C-1H spin state selective experiments
31442D JNN-COSY
115513C-1H spin state selective experiments
116613C-1H spin state selective experiments

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.3mM TAR, 1.3mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 100% D2O100% D2O
21.1mM TAR, 1.1mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.37mM [U-98% 13C; U-98% 15N] TAR, 0.74mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.74mM TAR, 0.37mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
51.6mM TAR, 0.8mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 100% D2O100% D2O
60.5mM [U-98% 13C; U-98% 15N] TAR, 1.0mM TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 100% D2O100% D2O
71.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 100% D2O100% D2O
81.8mM TAR, 0.9mM [U-98% 13C; U-98% 15N] TAR*GA, 10mM sodium phosphate, 50mM sodium chloride, 0.01mM EDTA, 0.4g/L sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMTAR1
1.3 mMTAR*GA1
10 mMsodium phosphate1
50 mMsodium chloride1
0.01 mMEDTA1
0.4 g/Lsodium azide1
1.1 mMTAR2
1.1 mMTAR*GA2
10 mMsodium phosphate2
50 mMsodium chloride2
0.01 mMEDTA2
0.4 g/Lsodium azide2
0.37 mMTAR[U-98% 13C; U-98% 15N]3
0.74 mMTAR*GA3
10 mMsodium phosphate3
50 mMsodium chloride3
0.01 mMEDTA3
0.4 g/Lsodium azide3
0.74 mMTAR4
0.37 mMTAR*GA[U-98% 13C; U-98% 15N]4
10 mMsodium phosphate4
50 mMsodium chloride4
0.01 mMEDTA4
0.4 g/Lsodium azide4
1.6 mMTAR5
0.8 mMTAR*GA[U-98% 13C; U-98% 15N]5
10 mMsodium phosphate5
50 mMsodium chloride5
0.01 mMEDTA5
0.4 g/Lsodium azide5
0.5 mMTAR[U-98% 13C; U-98% 15N]6
1.0 mMTAR*GA6
10 mMsodium phosphate6
50 mMsodium chloride6
0.01 mMEDTA6
0.4 g/Lsodium azide6
1.8 mMTAR7
0.9 mMTAR*GA[U-98% 13C; U-98% 15N]7
10 mMsodium phosphate7
50 mMsodium chloride7
0.01 mMEDTA7
0.4 g/Lsodium azide7
1.8 mMTAR8
0.9 mMTAR*GA[U-98% 13C; U-98% 15N]8
10 mMsodium phosphate8
50 mMsodium chloride8
0.01 mMEDTA8
0.4 g/Lsodium azide8
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1606.6ambient 298 K
2606.6ambient 283 K
3606.6ambient 278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
Felix2000Accelrys Software Inc.chemical shift assignment
Felix2000Accelrys Software Inc.processing
Insight IIAccelrys Software Inc.data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxpeak picking
Curves5.3Lavery, sklenar, 1989data analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH (Wimberly, 1992)
NMR constraintsNOE constraints total: 392
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 800 / Conformers submitted total number: 17

+
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://pdbjlc1.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