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- PDB-1q75: Solution structure of the dyskeratosis congenita mutant P2b hairp... -

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Basic information

Entry
Database: PDB / ID: 1q75
TitleSolution structure of the dyskeratosis congenita mutant P2b hairpin from human telomerase RNA
ComponentsDKC mutant P2b telomerase RNA
KeywordsRNA / TETRALOOP / PENTALOOP / UUCG / YNMG
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTheimer, C.A. / Finger, L.D. / Feigon, J.
Citation
Journal: Rna / Year: 2003
Title: YNMG tetraloop formation by a dyskeratosis congenita mutation in human telomerase RNA.
Authors: Theimer, C.A. / Finger, L.D. / Feigon, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA
Authors: Theimer, C.A. / Finger, L.D. / Trantirek, L. / Feigon, J.
History
DepositionAug 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DKC mutant P2b telomerase RNA


Theoretical massNumber of molelcules
Total (without water)4,7841
Polymers4,7841
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 DKC mutant P2b telomerase RNA


Mass: 4783.889 Da / Num. of mol.: 1 / Mutation: G107A, C108G / Source method: obtained synthetically
Details: THE RNA WAS CHEMICALLY SYNTHESIZED using in vitro transcription with T7 RNA polymerase and a partially double-stranded DNA template. THE SEQUENCE OF THE RNA IS NATURALLY FOUND IN HOMO ...Details: THE RNA WAS CHEMICALLY SYNTHESIZED using in vitro transcription with T7 RNA polymerase and a partially double-stranded DNA template. THE SEQUENCE OF THE RNA IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN) who have a certain type of autosomal dominant dyskeratosis congenita.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY (1,1echo and WATERGATE)
2222D 15N-HMQC, 2D 15N-CPMG-NOESY, 2D JNN-HNN-COSY
3332D NOESY, 2D TOCSY
44431P-spin echo difference CT HSQC
4543D 13C-NOESY HMQC, 2D 13C-HMQC,2D (H)CCH COSY, 3D (H)CCH TOCSY
464CT-CE-HSQC
NMR detailsText: CT-CE-HSQC was used for determining residual dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM unlabeled RNA, 10mM sodium phosphate buffer, pH 6.3, 200mM KCl, 50uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O95% H2O/5% D2O
21mM 13C,15N-labeled RNA, 10mM sodium phosphate buffer, pH 6.3, 200mM KCl, 50uM EDTA, 0.2% sodium azide, 95% H2O,5% D2O95% H2O/5% D2O
31mM unlabeled RNA, 10mM sodium phosphate buffer, pH 6.3, 200mM KCl, 50uM EDTA, 0.2% sodium azide, 100% D2O100% D2O
41mM 13C,15N-labeled RNA, 10mM sodium phosphate buffer, pH 6.3, 200mM KCl, 50uM EDTA, 0.2% sodium azide, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200mM KCl 6.3ambient 283 K
2200mM KCl 6.3ambient 283 K
3200mM KCl 6.3ambient 293 K
4200mM KCl 6.3ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
AURELIA3.108Brungerdata analysis
X-PLOR3.851NIHstructure solution
X-PLOR3.851NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 283 NOE-derived distance constraints, 86 dihedral angle restraints, 16 distance restraints from hydrogen bonds, and 14 H-C residual dipolar couplings.
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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