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- PDB-2krl: The ensemble of the solution global structures of the 102-nt ribo... -

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Basic information

Entry
Database: PDB / ID: 2krl
TitleThe ensemble of the solution global structures of the 102-nt ribosome binding structure element of the turnip crinkle virus 3' UTR RNA
ComponentsRNA (102-MER)
KeywordsRNA / SAXS / 3' UTR / global structure of large RNAs
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTurnip crinkle virus
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing, duplex-orientation restrained
Model detailsclosest to the average, model 1
AuthorsZuo, X. / Wang, J. / Yu, P. / Eyler, D. / Xu, H. / Starich, M. / Tiede, D. / Simon, A. / Kasprzak, W. / Schwieters, C. / Shapiro, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus.
Authors: Zuo, X. / Wang, J. / Yu, P. / Eyler, D. / Xu, H. / Starich, M.R. / Tiede, D.M. / Simon, A.E. / Kasprzak, W. / Schwieters, C.D. / Shapiro, B.A. / Wang, Y.X.
History
DepositionDec 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (102-MER)


Theoretical massNumber of molelcules
Total (without water)32,9791
Polymers32,9791
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (102-MER)


Mass: 32978.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Turnip crinkle virus / References: GenBank: M22445.2

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Experimental details

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Experiment

Experiment
MethodDetails
SOLUTION NMRThe global structure of the TCV RNA was determined using the G2G method.
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-1H NOESY
1222D HNN-COSY
234IPAP-HSQC
NMR detailsText: MORE DETAILS ON STRUTURE DETERMINATION IN REMARK 265

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Sample preparation

Details
Solution-IDContentsSolvent system
10.06 mM RNA-1, 90% H2O/10% D2O90% H2O/10% D2O
20.3-0.8 mM [U-98% 15N] RNA-2, 90% H2O/10% D2O90% H2O/10% D2O
30.3-0.8 mM RNA-3, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-98% 15N] RNA-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.06 mMRNA-11
mMRNA-2[U-98% 15N]0.3-0.82
mMRNA-30.3-0.83
0.5 mMRNA-4[U-98% 15N]4
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298.2 K

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Data collection

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz
Soln scatterType: x-ray / Buffer name: 50 MM TRIS, 0.5 MM MgCl2 / Conc. range: 1.0-5.0
Data analysis software list: GNOM, HOME-WRITTEN SCRIPTS IN IGOR AND MATLAB
Data reduction software list: MARDETECTOR, HOME-WRITTEN PROGRAM
Detector specific: MARRESEARCH GMBH, GERMANY / Detector type: MARCCD 165 / Mean guiner radius: 30.9 nm / Mean guiner radius esd: 0.4 nm / Num. of time frames: 20 / Protein length: 110 / Sample pH: 6.8 / Source beamline: 12-ID,18-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K

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Processing

NMR software
NameVersionDeveloperClassification
G2G1(G2G) J. Wang, X. Zuo and Y-X. Wanggenerate global structure of rnas
X-PLOR NIH2.22Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, duplex-orientation restrained / Software ordinal: 1
Details: the orientations of all duplexes were restrained during the SA calculation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10
Soln scatter modelMethod: SIMULATED ANNEALING METHOD WITH RESTRAINTS OF X-RAY SCATTERING DATA, RDC DATA, GENERIC A-FORM GEOMETRIC DISTANCE IN DUPLEXES, GENERIC A-FORM LIKE STACKING, NMR DETECTED HYDROGEN BONDS, AND ...Method: SIMULATED ANNEALING METHOD WITH RESTRAINTS OF X-RAY SCATTERING DATA, RDC DATA, GENERIC A-FORM GEOMETRIC DISTANCE IN DUPLEXES, GENERIC A-FORM LIKE STACKING, NMR DETECTED HYDROGEN BONDS, AND SAXS MOLECULAR ENVELOPE DIMENISIONAL MEASUREMENTS.
Conformer selection criteria: STRUCTURES WITH LOWEST TOTAL ENERGY. THE TOTAL ENERGY INCLUDES PSEUDO-POTENTIALS OF SCATTERING TERM, RDC TERM, HYDROGEN BONDING TERM, AND OTHER REGULAR PSEUDO-POTENTIALS ...Conformer selection criteria: STRUCTURES WITH LOWEST TOTAL ENERGY. THE TOTAL ENERGY INCLUDES PSEUDO-POTENTIALS OF SCATTERING TERM, RDC TERM, HYDROGEN BONDING TERM, AND OTHER REGULAR PSEUDO-POTENTIALS IMPLEMENTED IN XPLOR-NIH.
Details: SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE. REFERENCE OF G2G IS : X. Zuo, J. Wang, P. ...Details: SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE. REFERENCE OF G2G IS : X. Zuo, J. Wang, P. Yu, D. Eyler, H. Xu, M.R. Starich, D.M. Tiede, A.E. Simon, W. Kasprzak, C.D. Schwieters, B.A. Shapiro, Y.-X. WANG, A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements; JOURNAL OF MOLECULAR BIOLOGY 2009, 393(3), 717-734.
Entry fitting list: G2G INITIAL STRUCTURE / Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1
Software list: G2G, DAMMIN AND DAMAVER IN ATSAS 2.1, XPLOR-NIH

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