[English] 日本語
Yorodumi
- PDB-1efs: CONFORMATION OF A DNA-RNA HYBRID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1efs
TitleCONFORMATION OF A DNA-RNA HYBRID
Components
  • DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*GP*AP*A)-3')
  • RNA (5'-R(*UP*UP*CP*UP*CP*UP*UP*CP*CP*UP*CP*UP*C)-3')
KeywordsDNA-RNA HYBRID / RNA-DNA hybrid duplex / DNA-RNA COMPLEX
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular mechanics distance geometry matrix relaxation
AuthorsLarue, V. / Hantz, E.
CitationJournal: Int.J.Biol.Macromol. / Year: 2001
Title: Solution conformation of an RNA--DNA hybrid duplex containing a pyrimidine RNA strand and a purine DNA strand.
Authors: Hantz, E. / Larue, V. / Ladam, P. / Le Moyec, L. / Gouyette, C. / Huynh Dinh, T.
History
DepositionFeb 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
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: DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*GP*AP*A)-3')
B: RNA (5'-R(*UP*UP*CP*UP*CP*UP*UP*CP*CP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,0522
Polymers8,0522
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)10 / 10back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #3closest to the average

-
Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*GP*AP*A)-3')


Mass: 4122.724 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*UP*UP*CP*UP*CP*UP*UP*CP*CP*UP*CP*UP*C)-3')


Mass: 3929.294 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
332DQF-COSY
442Reverse 1H-31P COSY
5521H-13C HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM each strand; 150mM NaCl, 0.1 mM EDTA, pH 7, 90% H2O,10% D2O90% H2O/10% D2O
21.2mM each strand; 150mM NaCl, 0.1 mM EDTA, pH 7, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
180 mM NaCl 7ambient 278 K
280 mM NaCl 7ambient 291 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bcollection
Felix95data analysis
JUMNA10LAVERY, R.structure solution
IRMA95refinement
RefinementMethod: molecular mechanics distance geometry matrix relaxation
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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