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- PDB-1k6g: Solution Structure of Conserved AGNN Tetraloops: Insights into Rn... -

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Basic information

Entry
Database: PDB / ID: 1k6g
TitleSolution Structure of Conserved AGNN Tetraloops: Insights into Rnt1p RNA Processing
ComponentsRNA (5'-R(P*GP*GP*CP*GP*UP*CP*AP*UP*GP*AP*GP*UP*CP*CP*AP*UP*GP*GP*CP*GP*CP*C)-3')
KeywordsRNA / RNA Tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLebars, I. / Lamontagne, B. / Yoshizawa, S. / Abou Elela, S. / Fourmy, D.
CitationJournal: EMBO J. / Year: 2001
Title: Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing.
Authors: Lebars, I. / Lamontagne, B. / Yoshizawa, S. / Aboul-Elela, S. / Fourmy, D.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,0651
Polymers7,0651
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 / 25structures with the lowest energy
RepresentativeModel #1

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Components

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


Mass: 7065.242 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 NOESY
1312D DQF-COSY
1422D TOCSY
1533D NOESY-HMQC
1633D (H)CCH-TOCSY
173HP COSY
184HSQC
294HSQC
11043D HCP
2114HNN COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RNA, 10mM Na Phosphate, pH 6.4100% D2O
21mM RNA, 10mM Na Phosphate, pH 6.495% H20-5% D20
31mM RNA, 15N,13C, 10mM Na Phosphate, pH 6.4100% D2O
41mM RNA, 15N,13C, 10mM Na Phosphate, pH 6.495% H20-5% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Na Phosphate 6.4ambient 293 K
210 mM Na Phosphate 6.4ambient 278 K
310 mM Na Phosphate 6.4ambient 293 K
410 mM Na Phosphate 6.4ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameClassification
XwinNMRcollection
XwinNMRprocessing
AURELIAdata analysis
Discoverstructure solution
Discoverrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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