[English] 日本語
Yorodumi
- PDB-2o33: Solution structure of U2 snRNA stem I from S. cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o33
TitleSolution structure of U2 snRNA stem I from S. cerevisiae
ComponentsU2 snRNA
KeywordsRIBONUCLEIC ACID / RNA / Wobble base-pairs / U2 snRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSashital, D.G. / Venditti, V. / Angers, C.A. / Cornilescu, G. / Butcher, S.E.
CitationJournal: Rna / Year: 2007
Title: Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human.
Authors: Sashital, D.G. / Venditti, V. / Angers, C.G. / Cornilescu, G. / Butcher, S.E.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U2 snRNA


Theoretical massNumber of molelcules
Total (without water)6,2921
Polymers6,2921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain U2 snRNA


Mass: 6291.679 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The RNA was transcribed in vitro from a DNA oligonucleotide template using T7 RNA polymerase. The first two base pairs (U-A/C-G) have been substituted with G-C pairs to optimize transcription yields.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
1332D HNC(O)
2442D HCC
2542D 13C-1H CT-HSQC
2643D 13C-separated TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM unlabeled RNA; 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM unlabeled RNA; 50 mM NaCl; 99.99% D2O99.99% D2O
30.5 mM 13C/15N RNA; 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
40.5 mM 13C/15N RNA; 50 mM NaCl; 99.99% D2O99.99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 7ambient 283 K
250 mM NaCl 7ambient 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grossekunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenstructure solution
X-PLOR2.11.0Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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