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- PDB-2mhi: Solution structure of the CR4/5 domain of medaka telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 2mhi
TitleSolution structure of the CR4/5 domain of medaka telomerase RNA
ComponentsMedaka telomerase RNA
KeywordsRNA / CR4-CR5 / telomerase RNA / three-way junction / vertebrate / medaka
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKim, N. / Zhang, Q. / Feigon, J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure and sequence elements of the CR4/5 domain of medaka telomerase RNA important for telomerase function.
Authors: Kim, N.K. / Zhang, Q. / Feigon, J.
History
DepositionNov 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
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: Medaka telomerase RNA


Theoretical massNumber of molelcules
Total (without water)16,9921
Polymers16,9921
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 Medaka telomerase RNA


Mass: 16992.027 Da / Num. of mol.: 1 / Fragment: CR4/5 domain / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2132D 1H-15N HSQC
1232D 1H-13C HSQC
1342D 1H-13C HSQC
1452D 1H-13C HSQC
1562D 1H-13C HSQC
1672D 1H-13C HSQC
1722D DQF-COSY
1822D 1H-1H COSY
2912D 1H-1H NOESY
11022D 1H-1H NOESY
21192D 1H-1H NOESY
11282D 1H-1H NOESY
11322D 1H-1H TOCSY
11443D (H)CCH-TOCSY
11553D (H)CCH-TOCSY
11663D (H)CCH-TOCSY
11723D (H)CCH-TOCSY
21832D HNN-COSY
11942D 1H-1H filter/edited NOESY
12052D 1H-1H filter/edited NOESY
12162D 1H-1H filter/edited NOESY
12272D 1H-1H filter/edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
31 mM [U-13C; U-15N] mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-13C; U-15N]-Ade mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
51 mM [U-13C; U-15N]-Ura mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
61 mM [U-13C; U-15N]-Gua mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
71 mM [U-13C; U-15N]-Cyt mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
81.5 mM [U-2H] mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 100% D2O100% D2O
91.5 mM [U-2H] mdCR4/5, 10 mM sodium phosphate, 100 mM potassium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMmdCR4/5-11
10 mMsodium phosphate-21
100 mMpotassium chloride-31
1.2 mMmdCR4/5-42
10 mMsodium phosphate-52
100 mMpotassium chloride-62
1 mMmdCR4/5-7[U-13C; U-15N]3
10 mMsodium phosphate-83
100 mMpotassium chloride-93
1 mMmdCR4/5-10[U-13C; U-15N]-Ade4
10 mMsodium phosphate-114
100 mMpotassium chloride-124
1 mMmdCR4/5-13[U-13C; U-15N]-Ura5
10 mMsodium phosphate-145
100 mMpotassium chloride-155
1 mMmdCR4/5-16[U-13C; U-15N]-Gua6
10 mMsodium phosphate-176
100 mMpotassium chloride-186
1 mMmdCR4/5-19[U-13C; U-15N]-Cyt7
10 mMsodium phosphate-207
100 mMpotassium chloride-217
1.5 mMmdCR4/5-22[U-2H]8
10 mMsodium phosphate-238
100 mMpotassium chloride-248
1.5 mMmdCR4/5-25[U-2H]9
10 mMsodium phosphate-269
100 mMpotassium chloride-279
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 6.3 ambient 293 K
210 6.3 ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
XwinNMR3.5Bruker Biospindata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
MOLMOLKoradi, Billeter and Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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