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- PDB-1zc5: Structure of the RNA signal essential for translational frameshif... -

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Basic information

Entry
Database: PDB / ID: 1zc5
TitleStructure of the RNA signal essential for translational frameshifting in HIV-1
ComponentsHIV-1 frameshift RNA signal
KeywordsRNA / RNA bulged helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGaudin, C. / Mazauric, M.H. / Traikia, M. / Guittet, E. / Yoshizawa, S. / Fourmy, D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the RNA Signal Essential for Translational Frameshifting in HIV-1
Authors: Gaudin, C. / Mazauric, M.H. / Traikia, M. / Guittet, E. / Yoshizawa, S. / Fourmy, D.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 29, 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: HIV-1 frameshift RNA signal


Theoretical massNumber of molelcules
Total (without water)13,2511
Polymers13,2511
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 / 23structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain HIV-1 frameshift RNA signal


Mass: 13250.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic-T7 RNA transcript

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D TOCSY, DQF-COSY, HP COSY
2333D-(H)CCH-TOCSY, HSQC, 3D HCP

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RNA, 10mM Na phosphate buffer pH=6.4, 90% H2O, 10% D2O90% H2O/10% D2O
21mM RNA, 10mM Na phosphate buffer pH=6.4, 100% D2O100% D2O
31mM RNA 15N, 13C, 10mM Na phosphate buffer pH=6.4, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM Na phosphate 6.4 ambient 283 K
210mM Na phosphate 6.4 ambient 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1processing
Gifa4.4Delsuc, M.A.data analysis
AURELIAdata analysis
Sparky3.11data analysis
Discoverrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 23 / Conformers submitted total number: 20

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