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- PDB-2euy: Solution structure of the internal loop of human U65 H/ACA snoRNA... -

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Basic information

Entry
Database: PDB / ID: 2euy
TitleSolution structure of the internal loop of human U65 H/ACA snoRNA 3' hairpin
ComponentsU65 box H/ACA snoRNA
KeywordsRNA / haripin / internal-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsFeigon, J. / Khanna, M. / Wu, H. / Johansson, C. / Caizergues-Ferrer, M.
CitationJournal: Rna / Year: 2006
Title: Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA.
Authors: Khanna, M. / Wu, H. / Johansson, C. / Caizergues-Ferrer, M. / Feigon, J.
History
DepositionOct 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: U65 box H/ACA snoRNA


Theoretical massNumber of molelcules
Total (without water)10,9711
Polymers10,9711
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)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain U65 box H/ACA snoRNA


Mass: 10970.566 Da / Num. of mol.: 1
Fragment: RNA hairpin containing the 3' internal-loop (pseudouridylation pocket)
Source method: obtained synthetically / Details: This sequence occurs naturally in humans

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
1433D (H)CCH-TOCSY
1533D (H)CCH-COSY
16313C-filtered/edited 2D NOESYs

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Sample preparation

Details
Solution-IDContentsSolvent system
1unlabeled10% D2O, 90% H2O
2unlabeled99.999% D2O
3G,A,U,or C-selectively 13C,15N-labled99.999% D2O
Sample conditionsIonic strength: 10mM sodium phosphate buffer / pH: 6 / Pressure: ambient / Temperature: 293 K

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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
XwinNMR3.5Brukercollection
Felix2000Accelrydata analysis
X-PLORNIHClorerefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structure was refined against 11 residual dipolar coupling rstraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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