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- PDB-2pcw: Solution Structure of an rRNA Substrate Bound to the Pseudouridyl... -

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Basic information

Entry
Database: PDB / ID: 2pcw
TitleSolution Structure of an rRNA Substrate Bound to the Pseudouridylation Pocket of a Box H/ACA snoRNA
Components
  • U65 box H/ACA snoRNA
  • rRNA substrate of U65 box H/ACA snoRNA
KeywordsRNA / box H/ACA snoRNA / pseudouridylation pocket / rRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics molecular dynamics
AuthorsJin, H. / Loria, J.P. / Moore, P.B.
CitationJournal: Mol.Cell / Year: 2007
Title: Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA.
Authors: Jin, H. / Loria, J.P. / Moore, P.B.
History
DepositionMar 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
B: rRNA substrate of U65 box H/ACA snoRNA


Theoretical massNumber of molelcules
Total (without water)15,7292
Polymers15,7292
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)17 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain U65 box H/ACA snoRNA


Mass: 11233.758 Da / Num. of mol.: 1
Fragment: RNA Hairpin containing the 5' pseudouridylation pocket
Source method: obtained synthetically
Details: Synthesized by in-vitro transcription using T7 RNA polymerase from linearzed plsmid DNA. This sequence occurs naturally in humans.
#2: RNA chain rRNA substrate of U65 box H/ACA snoRNA


Mass: 4495.691 Da / Num. of mol.: 1
Fragment: rRNA substrate of the 5' pseudouridylation pocket of U65 Box H/ACA snoRNA
Source method: obtained synthetically
Details: Chemically synthesized. 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
2212D NOESY
231DQF-COSY
14215N-HSQC
25213C-HSQC
16215N-NOESYHSQC
27213C-NOESYHSQC
282(H)CCH/COSY/RELAY/TOCSY
29131P-HETCOR
NMR detailsText: See paper for more details

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Sample preparation

Details
Solution-IDContentsSolvent system
1Unlabeled90% H2O/10% D2O
2Uniform labeling with 15N: U-15N Uniform labeling with 13C: U-13C90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM cacodylate, 1mM MgCl2, 50 mM NaCl, 0.1 mM EDTA. 6.5ambient 283 K
25 mM cacodylate, 1mM MgCl2, 50 mM NaCl, 0.1 mM EDTA 6.5ambient 303 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
Varian INOVAVarianINOVA5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeprocessing
Sparkydata analysis
CNS1.1BRUNGERrefinement
RefinementMethod: torsion angle dynamics molecular dynamics / Software ordinal: 1 / Details: Described in the primary citation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 17

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