[English] 日本語
Yorodumi
- PDB-1nc0: U80G U6 Intramolecular Stem-Loop RNA from Saccharomyces cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nc0
TitleU80G U6 Intramolecular Stem-Loop RNA from Saccharomyces cerevisiae
ComponentsU80G U6 RNA Intramolecular Stem-Loop
KeywordsRNA / U6 RNA / U80G / Residual Dipolar Coupling / RDC
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics molecular dynamics residual dipolar couplings
AuthorsSashital, D.G. / Allmann, A.M. / Van Doren, S. / Butcher, S.E.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Basis for a Lethal Mutation in U6 RNA
Authors: Sashital, D.G. / Allmann, A.M. / Van Doren, S. / Butcher, S.E.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U80G U6 RNA Intramolecular Stem-Loop


Theoretical massNumber of molelcules
Total (without water)7,7081
Polymers7,7081
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)18 / -
Representative

-
Components

#1: RNA chain U80G U6 RNA Intramolecular Stem-Loop


Mass: 7707.655 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcription using purified T7 RNA polymerase and synthetic DNA oligonucleotides.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
2432D H-13C HSQC 13C coupled
2542D H-13C HSQC 13C coupled

-
Sample preparation

Details
Solution-IDContentsSolvent system
1U80G U6 ISL90% D2O, 10% H2O
2U80G U6 ISL99% D2O
3U80G U6 ISL-13C/15N90% D2O, 10% H2O
4U80G U6 ISL-13C/15N, 17 mg/mL pf1 phage90% D2O, 10% H2O
Sample conditions
Conditions-IDpHTemperature (K)
16.5283 K
26.5303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503
Bruker DMXBrukerDMX4004

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T. et. al.structure solution
X-PLOR3.843Brungerrefinement
RefinementMethod: torsion angle dynamics molecular dynamics residual dipolar couplings
Software ordinal: 1
Details: The structures are based on 474 NOE derived distance constraints, 179 dihedral angle restraints, and 24 restraints from hydrogen bonds.
NMR ensembleConformers submitted total number: 18

+
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