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- PDB-2m23: NMR solution structure of the d3'-hairpin of the group II intron ... -

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Basic information

Entry
Database: PDB / ID: 2m23
TitleNMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1
Components
  • RNA (29-MER)
  • RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_
KeywordsRNA / group II intron / ribozyme / hairpin / EBS1 / IBS1 / splicing / 5'-splice site
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
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: 2K64
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (29-MER)
B: RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_


Theoretical massNumber of molelcules
Total (without water)11,4992
Polymers11,4992
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area894 Å2
ΔGint-2.8 kcal/mol
Surface area6209 Å2
MethodPISA
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: sequence produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: RNA chain RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_


Mass: 2197.355 Da / Num. of mol.: 1 / Fragment: IBS1 / Mutation: U61G, U63G / Source method: obtained synthetically

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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 NOESY
1312D 1H-1H TOCSY
1452D 1H-1H NOESY
1542D 1H-13C HSQC aliphatic
1662D 1H-13C HSQC aliphatic
2742D 1H-15N HSQC
1842D 1H-13C HSQC aromatic
1962D 1H-13C HSQC aromatic
11032D 1H-13C HSQC aliphatic
11132D 1H-13C HSQC aromatic
21222D 1H-1H NOESY
21322D 1H-1H NOESY
31422D 1H-1H NOESY
21542D JNN HNN COSY
11611D-31P
1174F1,2 X-filtered 1H-1H NOESY
1184F1,2 X-filtered 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
40.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
50.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
60.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (29-MER)-10.5-0.91
mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-20.5-0.91
110 mMpotassium chloride-31
10 uMEDTA-41
mMRNA (29-MER)-50.5-0.92
mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-60.5-0.92
110 mMpotassium chloride-72
10 uMEDTA-82
0.5 mMRNA (29-MER)-9[U-100% 13C; U-100% 15N]3
0.5 mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-103
110 mMpotassium chloride-113
10 uMEDTA-123
0.5 mMRNA (29-MER)-13[U-100% 13C; U-100% 15N]4
0.5 mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-144
110 mMpotassium chloride-154
10 uMEDTA-164
0.6 mMRNA (29-MER)-17[3',4',5',5'',5-100% 2H]5
0.6 mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-185
110 mMpotassium chloride-195
10 uMEDTA-205
0.5 mMRNA (29-MER)-21[U-100% 13C; U-100% 15N]6
0.5 mMRNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3')-226
110 mMpotassium chloride-236
10 uMEDTA-246
25.6 mg/mLPf1 phage-256
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1110 6.8 ambient 298 K
2110 6.8 ambient 278 K
3110 6.8 ambient 293 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
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
TopSpin1.3, 2.0, 2.1Bruker Biospincollection
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
DYANA1.5Guntert, Braun and Wuthrichdata analysis
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
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: 34 / NA beta-angle constraints total count: 27 / NA chi-angle constraints total count: 36 / NA delta-angle constraints total count: 32 / NA epsilon-angle constraints total count: 28 / NA gamma-angle constraints total count: 28 / NA other-angle constraints total count: 33 / NA sugar pucker constraints total count: 96 / NOE constraints total: 747 / NOE intraresidue total count: 250 / NOE sequential total count: 348 / Hydrogen bond constraints total count: 82
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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