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- PDB-2lhp: High resolution NMR solution structure of helix H1 of the chimpan... -

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Basic information

Entry
Database: PDB / ID: 2lhp
TitleHigh resolution NMR solution structure of helix H1 of the chimpanzee HAR1 RNA
ComponentsRNA (37-MER)
KeywordsRNA / UUCG tetraloop / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesPan troglodytes (chimpanzee)
MethodSOLUTION NMR / simulated annealing, energy minimization
Model detailslowest energy, model 1
AuthorsCevec, M. / Ziegeler, M. / Richter, C. / Schwalbe, H.
CitationJournal: Chembiochem / Year: 2012
Title: NMR Studies of HAR1 RNA Secondary Structures Reveal Conformational Dynamics in the Human RNA.
Authors: Ziegeler, M. / Cevec, M. / Richter, C. / Schwalbe, H.
History
DepositionAug 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
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 / 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 (37-MER)


Theoretical massNumber of molelcules
Total (without water)11,8721
Polymers11,8721
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (37-MER)


Mass: 11872.081 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription using T7 RNA polymerase and DNA oligonucleotide template
Source: (synth.) Pan troglodytes (chimpanzee)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-15N HSQC
2222D HNN-COSY
2312D 1H-1H NOESY
1443D 1H-13C-13C-TROSY relayed (H)CCH-COSY
1552D 1H-13C HSQC
1612D 1H-1H NOESY
1712D DQF-COSY
2853D 1H-13C NOESY
2932D 1H-13C HCCNH-TOCSY
11053D HCP
11152D 1H-31P COSY
11253D forward-directed HCC-TOCSY-CCH E.COSY
11352D H(C)N
21442D HNCO
11553D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM RNA (37-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 15N] RNA (37-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-13C; U-15N]-Ade,Ura RNA (37-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-13C; U-15N]-Cyt,Gua RNA (37-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
51 mM [U-13C; U-15N]-Cyt,Gua RNA (37-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRNA (37-MER)-11
50 mMpotassium chloride-21
25 mMpotassium phosphate-31
0.4 mMRNA (37-MER)-4[U-100% 15N]2
50 mMpotassium chloride-52
25 mMpotassium phosphate-62
0.3 mMRNA (37-MER)-7[U-13C; U-15N]-Ade,Ura3
50 mMpotassium chloride-83
25 mMpotassium phosphate-93
1 mMRNA (37-MER)-10[U-13C; U-15N]-Cyt,Gua4
50 mMpotassium chloride-114
25 mMpotassium phosphate-124
1 mMRNA (37-MER)-13[U-13C; U-15N]-Cyt,Gua5
50 mMpotassium chloride-145
25 mMpotassium phosphate-155
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1756.2ambient 298 K
2756.2ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE7004
Bruker AvanceBrukerAVANCE6005

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.113Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
NMR constraintsNOE constraints total: 727
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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