[English] 日本語
Yorodumi
- PDB-1lc6: Solution Structure of the U6 Intramolecular Stem-loop RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lc6
TitleSolution Structure of the U6 Intramolecular Stem-loop RNA
ComponentsU6 Intramolecular Stem-loop RNA
KeywordsRNA / stem-loop / pentaloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle molecular dynamics, cartesian space simulated annealing, molecular dynamics
AuthorsHuppler, A. / Nikstad, L.J. / Allmann, A.M. / Brow, D.A. / Butcher, S.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure.
Authors: Huppler, A. / Nikstad, L.J. / Allmann, A.M. / Brow, D.A. / Butcher, S.E.
History
DepositionApr 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: U6 Intramolecular Stem-loop RNA


Theoretical massNumber of molelcules
Total (without water)7,6691
Polymers7,6691
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)40 / 100structures with the lowest energy
RepresentativeModel #40lowest energy

-
Components

#1: RNA chain U6 Intramolecular Stem-loop RNA


Mass: 7668.615 Da / Num. of mol.: 1 / Mutation: A62G / Source method: obtained synthetically
Details: T7 RNA transcript from synthetic DNA. Sequence occurs in S. cerevisiae.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C-separated NOESY
NMR detailsText: Standard 2D and 3D homonuclear and heteronuclear techniques

-
Sample preparation

DetailsContents: 1 mM U6 ISL RNA, 13C15N, pH 7.0, 50 mM NaCl / Solvent system: 100% D2O and 90/10% H2O/D2O
Sample conditionsIonic strength: 50 mM / pH: 7 / Pressure: ambient / Temperature: 303 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 DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX5003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
DYANA1.5P.Guentert, C.Mumenthaler, T.Herrmannrefinement
Felix98Biosymdata analysis
X-PLOR3.1Axel Brungerstructure solution
Sparky3.72Thomas Goddarddata analysis
RefinementMethod: torsion angle molecular dynamics, cartesian space simulated annealing, molecular dynamics
Software ordinal: 1
Details: Structure based on 521 NOEs, 145 dihedral angles and 25 H-bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

+
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