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- PDB-1byx: CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE ... -

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Basic information

Entry
Database: PDB / ID: 1byx
TitleCHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JUNCTION FORMED DURING INITIATION OF HIV-1 REVERSE TRANSCRIPTION
Components
  • DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')
  • RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
KeywordsDNA-RNA HYBRID / RNA:RNA-DNA CHIMERIC HYBRID / RNASE H / REVERSE TRANSCRIPTASE / DNA-RNA COMPLEX
Function / homologyDNA/RNA hybrid / RNA
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsSzyperski, T. / Goette, M. / Billeter, M. / Perola, E. / Cellai, L.
CitationJournal: J.Biomol.NMR / Year: 1999
Title: NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription.
Authors: Szyperski, T. / Gotte, M. / Billeter, M. / Perola, E. / Cellai, L. / Heumann, H. / Wuthrich, K.
History
DepositionOct 20, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0332
Polymers5,0332
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)20 / 100DYANA TARGET FUNCTION
Representative

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Components

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


Mass: 2581.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE RNA:RNA-DNA CHIMERIC HYBRID DUPLEX WAS CHEMICALLY SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY VIRUS TYPE 1 (HIV-1). THE DUPLEX IS FORMED DURING THE INITIATION OF (-)DNA STRAND SYNTHESIS IN HIV-1 REPLICATION.
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')


Mass: 2451.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHIMERIC HYBRID RNA/RNA-DNA DUPLEX

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
141E H-P HETCOR
151H-C COSY
NMR detailsText: THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER FORCE FIELD USING THE PROGRAM OPAL

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Sample preparation

Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002
Varian UNITYVarianUNITY7503

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS ARE DESCRIBED IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: DYANA TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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