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- PDB-2p89: Solution structure of the 3' pseudouridyation pocket of U65 snoRN... -

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Basic information

Entry
Database: PDB / ID: 2p89
TitleSolution structure of the 3' pseudouridyation pocket of U65 snoRNA with bound substrate
Components
  • 28S rRNA
  • U65 H/ACA snoRNA
KeywordsRNA / RNA-RNA complex / three-way junctions / double helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsWu, H. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification.
Authors: Wu, H. / Feigon, J.
History
DepositionMar 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 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: 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 H/ACA snoRNA
B: 28S rRNA


Theoretical massNumber of molelcules
Total (without water)15,3082
Polymers15,3082
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain U65 H/ACA snoRNA


Mass: 10970.566 Da / Num. of mol.: 1 / Fragment: 3' pseudouridylation pocket
Mutation: Additional UUCG tetraloop and G:C base pair at the end the helices
Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: RNA chain 28S rRNA


Mass: 4337.563 Da / Num. of mol.: 1 / Fragment: fragment 4423-4436 / Mutation: G4423U / 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
13213C-Filter/edited 2D NOESY
1423D 13C-separated NOESY
152HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM Sodium phosphate buffer, pH 6.090% H2O/10% D2O
25 mM Sodium phosphate buffer, pH 6.0D2O
Sample conditionsIonic strength: 5 mM / pH: 6 / Pressure: ambient / Temperature: 288 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
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
XwinNMR3.1Brukerprocessing
Sparky3.113T.D. Goddard and D. G. Knellerdata analysis
X-PLORNIHBrungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on 768 NOE-derived distance constraints, 404 dihedral angle restraints,106 distance restraints from hydrogen bonds, 32 RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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