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- PDB-2l3e: Solution structure of P2a-J2a/b-P2b of human telomerase RNA -

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Basic information

Entry
Database: PDB / ID: 2l3e
TitleSolution structure of P2a-J2a/b-P2b of human telomerase RNA
Components35-MER
KeywordsRNA / human telomerase RNA / hTR / P2a / P2b / J2ab
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, Q. / Kim, N. / Peterson, R.D. / Wang, Z. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Inaugural Article: Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA.
Authors: Zhang, Q. / Kim, N.K. / Peterson, R.D. / Wang, Z. / Feigon, J.
History
DepositionSep 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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: 35-MER


Theoretical massNumber of molelcules
Total (without water)11,1651
Polymers11,1651
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 35-MER


Mass: 11164.637 Da / Num. of mol.: 1 / 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 11echo NOESY
1212D WATERGATE NOESY
2372D 1H-1H NOESY
2472D 1H-1H TOCSY
1522D 1H-15N HSQC
2622D 1H-15N HSQC
2722D 1H-13C HSQC
2832D 13C Filtered/Edited NOESY
2942D 13C Filtered/Edited NOESY
21052D 13C Filtered/Edited NOESY
21162D 13C Filtered/Edited NOESY
21232D (H)CCH-COSY
21342D (H)CCH-COSY
21452D (H)CCH-COSY
21562D (H)CCH-COSY
21633D (H)CCH-TOCSY
21743D (H)CCH-TOCSY
21853D (H)CCH-TOCSY
21963D (H)CCH-TOCSY
22032D 1H-13C HSQC
22142D 1H-13C HSQC
22252D 1H-13C HSQC
22362D 1H-13C HSQC
22432D 31P spin echo difference CT-HSQC
22542D 31P spin echo difference CT-HSQC
22652D 31P spin echo difference CT-HSQC
22762D 31P spin echo difference CT-HSQC
22832D 31P spin echo difference CT-(H)CCH correlation
22942D 31P spin echo difference CT-(H)CCH correlation
23052D 31P spin echo difference CT-(H)CCH correlation
23162D 31P spin echo difference CT-(H)CCH correlation
23282D 1H-13C HSQC
23322D 1H-15N HSQC
23422D 1H-13C S3CT-HSQC
23522D 1H-13C S3CT-HSQC
13622D HNNOESY
23733D HCNCH
23843D HCNCH
23953D HCNCH
24063D HCNCH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM P2ab RNA (35-MER), 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-98% 13C; U-98% 15N] P2ab RNA (35-MER), 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-13C; U-15N]-Ade P2ab RNA (35-MER), 100% D2O100% D2O
41.0 mM [U-13C; U-15N]-Cyt P2ab RNA (35-MER), 100% D2O100% D2O
51.0 mM [U-13C; U-15N]-Gua P2ab RNA (35-MER), 100% D2O100% D2O
61.0 mM [U-13C; U-15N]-Ura P2ab RNA (35-MER), 100% D2O100% D2O
71.0 mM P2ab RNA (35-MER), 100% D2O100% D2O
81.0 mM [U-98% 13C; U-98% 15N] P2ab RNA (35-MER), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMP2ab RNA (35-MER)-11
1.0 mMP2ab RNA (35-MER)-2[U-98% 13C; U-98% 15N]2
1.0 mMP2ab RNA (35-MER)-3[U-13C; U-15N]-Ade3
1.0 mMP2ab RNA (35-MER)-4[U-13C; U-15N]-Cyt4
1.0 mMP2ab RNA (35-MER)-5[U-13C; U-15N]-Gua5
1.0 mMP2ab RNA (35-MER)-6[U-13C; U-15N]-Ura6
1.0 mMP2ab RNA (35-MER)-77
1.0 mMP2ab RNA (35-MER)-8[U-98% 13C; U-98% 15N]8
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11006.4ambient 283.15 K
21006.4ambient 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX6003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.8Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Sparky3.110.Goddardchemical shift assignment
Sparky3.110.Goddarddata analysis
Sparky3.110.Goddardprocessing
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 27 / NA beta-angle constraints total count: 25 / NA chi-angle constraints total count: 35 / NA delta-angle constraints total count: 35 / NA epsilon-angle constraints total count: 29 / NA gamma-angle constraints total count: 26 / NA other-angle constraints total count: 53 / NA sugar pucker constraints total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.041 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.08 Å / Maximum torsion angle constraint violation: 1.704 ° / Maximum upper distance constraint violation: 0.412 Å / Torsion angle constraint violation method: X-PLOR NIH
NMR ensemble rmsDistance rms dev: 0.018 Å / Distance rms dev error: 0.003 Å

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