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- PDB-2m24: NMR solution structure of the d3'-hairpin including the exon bind... -

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Basic information

Entry
Database: PDB / ID: 2m24
TitleNMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
ComponentsRNA (29-MER)
KeywordsRNA / group II intron / ribozyme / splicing / EBS1 / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsKruschel, D. / Skilandat, M. / Sigel, R.K.O.
CitationJournal: Rna / Year: 2014
Title: NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Authors: Kruschel, D. / Skilandat, M. / Sigel, R.K.
History
DepositionDec 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
SupersessionApr 16, 2014ID: 2K63
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)9,3021
Polymers9,3021
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (29-MER)


Mass: 9301.547 Da / Num. of mol.: 1 / Fragment: d3'EBS1 / Mutation: A15C, A17C / Source method: obtained synthetically
Details: the sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2422D 1H-1H NOESY
2522D 1H-1H NOESY
3632D 1H-13C HSQC aliphatic
3732D 1H-13C HSQC aromatic
2832D 1H-15N HSQC
3942D 1H-13C HSQC aliphatic
31042D 1H-13C HSQC aromatic
21132D JNN HNN COSY
41212D 1H-1H NOESY
31312D 1H-1H NOESY
11411D 31P
11562D 1H-1H NOESY
11652D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
40.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
50.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
60.6 mM [3',4',5',5'',5, 100% 2H] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (29-MER)-10.4-1.21
10 mMpotassium chloride-21
10 uMEDTA-31
mMRNA (29-MER)-40.4-1.22
10 mMpotassium chloride-52
10 uMEDTA-62
0.7 mMRNA (29-MER)-7[U-100% 13C; U-100% 15N]3
10 mMpotassium chloride-83
10 uMEDTA-93
0.7 mMRNA (29-MER)-10[U-100% 13C; U-100% 15N]4
10 mMpotassium chloride-114
10 uMEDTA-124
25.6 mg/mLPf1 phage-134
0.7 mMRNA (29-MER)-14[U-100% 13C; U-100% 15N]5
10 mMpotassium chloride-155
10 uMEDTA-165
0.6 mMRNA (29-MER)-17[3',4',5',5'',5, 100% 2H]6
10 mMpotassium chloride-186
10 uMEDTA-196
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1106.8ambient 293 K
2106.8ambient 278 K
3106.8ambient 298 K
4106.8ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3, 2.0, 2.1Bruker Biospincollection
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichdata analysis
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, torsion angle dynamics / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 28 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 29 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NA other-angle constraints total count: 27 / NA sugar pucker constraints total count: 48 / NOE constraints total: 511 / NOE intraresidue total count: 176 / NOE sequential total count: 250 / Hydrogen bond constraints total count: 45
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å

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