[English] 日本語
Yorodumi
- PDB-1hs3: SOLUTION STRUCTURE OF RNA HAIRPIN LOOP UUAAUU AS PART OF HAIRPIN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hs3
TitleSOLUTION STRUCTURE OF RNA HAIRPIN LOOP UUAAUU AS PART OF HAIRPIN R(GCGUUAAUUCGCA)
Components5'-R(*GP*CP*GP*UP*UP*AP*AP*UP*UP*CP*GP*CP*A)-3'
KeywordsRNA / ribonucleic acid / hairpin loop / RNA structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, energy minimization
AuthorsZhang, H. / Culyba, M. / Volkman, H. / Krugh, T.R.
CitationJournal: To be Published
Title: Structural Characterization of Six-Nucleotide RNA Hairpin loops: r(UUAAUU), r(UUAAAU), r(UUAACU)
Authors: Zhang, H. / Culyba, M. / Volkman, H. / Krugh, T.R.
History
DepositionDec 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*GP*CP*GP*UP*UP*AP*AP*UP*UP*CP*GP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)4,1181
Polymers4,1181
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)1 / 30average structure of 30 conformers
Representative

-
Components

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


Mass: 4118.486 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

-
Sample preparation

DetailsContents: 1 mM RNA oligomer - H2O; 3 mM RNA oligomer - D2O
Sample conditionsIonic strength: 0.1 M NaCl, 0.01 M sodium phosphate / pH: 7.0 / Pressure: 1.0 atm / Temperature: 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Discoverversion 2.98MSIstructure solution
Discoverversion 2.98MSIrefinement
RefinementMethod: restrained molecular dynamics, energy minimization / Software ordinal: 1
NMR ensembleConformer selection criteria: average structure of 30 conformers
Conformers calculated total number: 30 / 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