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- PDB-2m1v: NMR solution structure of the d3'-hairpin from the Sc.ai5gamma gr... -

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Basic information

Entry
Database: PDB / ID: 2m1v
TitleNMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid
Components
  • DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')_
  • RNA (29-MER)
KeywordsDNA/RNA / RNA / DNA / ribozyme / group II intron / hybrid / reverse splicing / retrohoming / DNA-RNA complex
Function / homologyDNA / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodSOLUTION NMR / molecular dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsSkilandat, M. / Sigel, R.K.O.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Role of Mg(II) in DNA Cleavage Site Recognition in Group II Intron Ribozymes: SOLUTION STRUCTURE AND METAL ION BINDING SITES OF THE RNADNA COMPLEX.
Authors: Skilandat, M. / Sigel, R.K.
History
DepositionDec 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
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)
B: DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')_


Theoretical massNumber of molelcules
Total (without water)11,4152
Polymers11,4152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area896 Å2
ΔGint-4 kcal/mol
Surface area6264 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 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 / Source method: obtained synthetically
Details: in vitro transcription from a synthetic double-stranded DNA template using T7 RNA Polymerase
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#2: DNA chain DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')_


Mass: 2113.410 Da / Num. of mol.: 1 / Fragment: dIBS1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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
1352D 1H-1H NOESY
1442D 1H-1H NOESY
1542D 1H-1H TOCSY
1632D 1H-15N HSQC
2722D 1H-15N HSQC
1862D 1H-13C HSQC aliphatic
1962D 1H-13C HSQC aromatic
31022D 1H-1H NOESY
21122D 1H-1H NOESY
11262D 1H-13C HSQC aliphatic
11362D 1H-13C HSQC aromatic
11411D 31P
1153F1, F2 X-filtered 1H-1H NOESY
1163F1, F2 X-filtered 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.6-0.9 mM RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
40.5-1.0 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
50.6-0.9 mM [3',4',5',5'',5]-100% 2H RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
60.6-0.9 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.7-1.0 mM DNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
70.5-1.0 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
80.5-1.0 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (29-MER)-10.6-0.91
mMDNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')-20.7-1.01
110 mMpotassium chloride-31
10 uMEDTA-41
mMRNA (29-MER)-50.6-0.92
mMDNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')-60.7-1.02
110 mMpotassium chloride-72
10 uMEDTA-82
mMRNA (29-MER)-9[U-100% 13C; U-100% 15N]0.6-0.93
mMDNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')-100.7-1.03
110 mMpotassium chloride-113
10 uMEDTA-123
mMRNA (29-MER)-130.5-1.04
10 mMpotassium chloride-144
10 uMEDTA-154
mMRNA (29-MER)-16[3',4',5',5'',5]-100% 2H0.6-0.95
mMDNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')-170.7-1.05
110 mMpotassium chloride-185
10 uMEDTA-195
mMRNA (29-MER)-20[U-100% 13C; U-100% 15N]0.6-0.96
mMDNA (5'-D(*CP*AP*GP*TP*GP*TP*C)-3')-210.7-1.06
110 mMpotassium chloride-226
10 uMEDTA-236
mMRNA (29-MER)-24[U-100% 13C; U-100% 15N]0.5-1.07
10 mMpotassium chloride-257
10 uMEDTA-267
mMRNA (29-MER)-270.5-1.08
10 mMpotassium chloride-288
10 uMEDTA-298
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
TopSpin3Bruker Biospinprocessing
TopSpin3Bruker Biospindata analysis
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichdata analysis
DYANA1.5Guntert, Braun and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.3Schwieters, 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: 22 / NA chi-angle constraints total count: 36 / NA delta-angle constraints total count: 26 / NA epsilon-angle constraints total count: 22 / NA gamma-angle constraints total count: 22 / NA other-angle constraints total count: 33 / NA sugar pucker constraints total count: 78 / NOE constraints total: 733 / NOE intraresidue total count: 240 / NOE sequential total count: 351 / 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: 18 / 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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