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- PDB-1f5u: SOLUTION STRUCTURE OF THE KISSING DIMER OF H3 GACG STEM-LOOP IN T... -

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Basic information

Entry
Database: PDB / ID: 1f5u
TitleSOLUTION STRUCTURE OF THE KISSING DIMER OF H3 GACG STEM-LOOP IN THE 5'-END DIMERIZATION SIGNAL OF MOLONEY MURINE LEUKEMIA VIRUS GENOMIC RNA
ComponentsRNA (5'-R(*GP*GP*UP*GP*GP*GP*AP*GP*AP*CP*GP*UP*CP*CP*CP*AP*CP*C)-3')
KeywordsRNA / Retrovirus / Moloney murine leukemia virus / dimerization / tetraloop / stem-loop / kissing dimer
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsKim, C.-H. / Tinoco Jr., I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: A retroviral RNA kissing complex containing only two G.C base pairs.
Authors: Kim, C.H. / Tinoco Jr., I.
History
DepositionJun 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2000Provider: 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,6052
Polymers11,6052
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)1 / 19averaged and energy-minimized structure based on 19 converged structures
RepresentativeModel #1averaged and energy-minimized structure based on 19 converged structures

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Components

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


Mass: 5802.522 Da / Num. of mol.: 2 / Fragment: 18 MER RNA SEQUENCE MIMICKING H3 GACG STEM-LOOP / Source method: obtained synthetically
Details: This sequence occurs naturally in Moloney murine leukemia virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
2322D NOESY
242DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM RNA sample, 10mM Sodium phosphate buffer pH 6.5, 100mM Sodium Chloride, 0.1 mM EDTA90% H2O/10% D2O
22 mM RNA sample, 10mM Sodium phosphate buffer pH 6.5, 100mM Sodium Chloride, 0.1 mM EDTA99.96 % D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6.5ambient 293 K
2100mM NaCl 6.5ambient 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR910901Brukercollection
XwinNMRBrukercollection
Felix95data analysis
X-PLOR3.1Axel Brungerstructure solution
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is based on a total of 852 restraints, 528 NOE-derived distance constraints, 324 dihedral constraints
NMR representativeSelection criteria: averaged and energy-minimized structure based on 19 converged structures
NMR ensembleConformer selection criteria: averaged and energy-minimized structure based on 19 converged structures
Conformers calculated total number: 19 / Conformers submitted total number: 1

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