[English] 日本語
Yorodumi
- PDB-1xv0: Solution NMR structure of RNA internal loop with three consecutiv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xv0
TitleSolution NMR structure of RNA internal loop with three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCGAAGCCG
Components
  • 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P)-3'
  • 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3'
KeywordsRNA / Thermodynamics and Structure / Base stacking and Hydrogen bonding / 3-GA motif
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR
AuthorsChen, G. / Znosko, B.M. / Kennedy, S.D. / Krugh, T.R. / Turner, D.H.
CitationJournal: Biochemistry / Year: 2005
Title: Solution Structure of an RNA Internal Loop with Three Consecutive Sheared GA Pairs
Authors: Chen, G. / Znosko, B.M. / Kennedy, S.D. / Krugh, T.R. / Turner, D.H.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
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: 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3'
B: 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P)-3'


Theoretical massNumber of molelcules
Total (without water)6,4572
Polymers6,4572
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / 40structures with the least restraint violations
RepresentativeModel #17closest to the average

-
Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3'


Mass: 3272.996 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P)-3'


Mass: 3183.991 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
231DQF-COSY
2412D NOESY

-
Sample preparation

DetailsContents: 80 mM NaCl, 10 mM Sodium phosphates, 0.5 mM EDTA, pH5.9 10% D2O
Solvent system: NMR
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.9 1 atm303 K
25.9 1 atm273 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionClassification
Felix2000data analysis
Discoverstructure solution
Discoverrefinement
Amberstructure solution
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 33

+
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