[English] 日本語
Yorodumi
- PDB-1o15: THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGUL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o15
TitleTHEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR COUPLINGS
ComponentsTHEOPHYLLINE-BINDING RNA
KeywordsRNA / RIBONUCLEIC ACID
Function / homologyTHEOPHYLLINE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsClore, G.M. / Kuszewski, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2003
Title: Improving the Accuracy of NMR Structures of RNA by Means of Conformational Database Potentials of Mean Force as Assessed by Complete Dipolar Coupling Cross-Validation
Authors: Clore, G.M. / Kuszewski, J.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Interlocking Structural Motifs Mediate Molecular Discrimination by a Theophylline-Binding RNA
Authors: Zimmermann, G.R. / Jenison, R.D. / Wick, C.L. / Simorre, J.P. / Pardi, A.
#2: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Refinement of Local and Long Range Structural Order in Theophylline-Binding RNA Using Using 13C-1H Residual Dipolar Couplings and Restrained Molecular Dynamics.
Authors: Sibille, N. / Pardi, A. / Simorre, J.P. / Blackledge, M.
#3: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Improving the Accuracy of NMR Structures of DNA by Means of a Database Potential of Mean Force Describing Base-Base Positional Interactions.
Authors: Kuszewski, J. / Schwieters, C. / Clore, G.M.
History
DepositionOct 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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_database_remark.text / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 8 THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE ARE SUMMARIZED AS FOLLOWS: DISTANCE ... THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE ARE SUMMARIZED AS FOLLOWS: DISTANCE RESTRAINTS 30 INTRARESIDUE NOES 86 SEQUENTIAL NOES 17 MEDIUM RANGE (1 < |i-j|<5) NOES 90 LONG RANGE (|i-j|>=5) NOES 52 DISTANCES FOR 8 W-C BASE PAIRS and 1 G-U WOBBLE PAIR TOTAL: 223 LOOSE TORSION ANGLE RESTRAINTS 31 DELTA 33 CHI 9 ALPHA, 9 BETA, 10 GAMMA, 9 EPSILON AND 9 ZETA TOTAL: 110. 13C-1H DIPOLAR COUPLINGS 55 SUGAR 46 BASE TOTAL 101

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THEOPHYLLINE-BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8192
Polymers10,6381
Non-polymers1801
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 250RESTRAINED REGULARIZED MEAN STRUCTURE
Representative

-
Components

#1: RNA chain THEOPHYLLINE-BINDING RNA


Mass: 10638.409 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CONSENSUS SEQUENCE OF THE THEOPHYLLINE BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP
#2: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND PARTITIONED IN A RATIO OF 70% (WORKING) AND 30% (TEST). 25 SIMULATED ANNEALING STRUCTURES ...Text: THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND PARTITIONED IN A RATIO OF 70% (WORKING) AND 30% (TEST). 25 SIMULATED ANNEALING STRUCTURES WERE CALCULATED FOR EACH PAIR, RESULTING IN A TOTAL OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN COORDINATES OF THE ENSEMBLE OF 250 INDIVIDUAL SIMULATED ANNEALING STRUCTURES CALCULATED WITH COMPLETE DIPOLAR COUPLING CROSS-VALIDATION. FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING DIPOLAR COUPLING R-FACTOR IS 8.6+/-0.5% AND THE FREE DIPOLAR COUPLING R-FACTOR IS 26.8+/-2.8%.

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

-
Processing

NMR softwareName: X-PLOR NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. THE EXPERIMENTAL RESTRAINTS ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. THE EXPERIMENTAL RESTRAINTS ARE ESSENTIALLY THE SAME AS THOSE LISTED IN N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE J.AM.CHEM.SOC. V 123, 12135 2001. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE, AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE.
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 250 / Conformers submitted total number: 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