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- PDB-1efs: CONFORMATION OF A DNA-RNA HYBRID -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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 7.0 ambient 278 K
280 mM NaCl 7.0 ambient 291 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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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

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