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- PDB-1l1w: NMR structure of a SRP19 binding domain in human SRP RNA -

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Entry
Database: PDB / ID: 1l1w
TitleNMR structure of a SRP19 binding domain in human SRP RNA
ComponentsSRP19 binding domain of SRP RNA
KeywordsRNA / RNA hairpin / tetraloop / GNRR / mismatch
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSakamoto, T. / Morita, S. / Tabata, K. / Nakamura, K. / Kawai, G.
CitationJournal: J.Biochem.(Tokyo) / Year: 2002
Title: Solution structure of a SRP19 binding domain in human SRP RNA.
Authors: Sakamoto, T. / Morita, S. / Tabata, K. / Nakamura, K. / Kawai, G.
History
DepositionFeb 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: SRP19 binding domain of SRP RNA


Theoretical massNumber of molelcules
Total (without water)9,4081
Polymers9,4081
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)1 / -
Representativeminimized average structure

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Components

#1: RNA chain SRP19 binding domain of SRP RNA


Mass: 9407.692 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is found naturally in Homo sapiens (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
1332D HNN-COSY
1442D half filtered NOESY
1552D half filtered NOESY
1662D half filtered NOESY
171DQF-COSY
1812D HP-COSY
1912D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM RNA fragment; 20mM phosphate buffer NA; 95% H2O, 5% D2O95% H2O/5% D2O
20.5mM RNA fragment; 20mM phosphate buffer NA; 100% D2O100% D2O
30.5mM RNA fragment U-15N,13C-Guanosine,Cytidine; 20mM phosphate buffer NA; 95% H2O, 5% D2O95% H2O/5% D2O
40.5mM RNA fragment U-15N,13C-Guanosine,Cytidine; 20mM phosphate buffer NA; 100% D2O100% D2O
50.5mM RNA fragment U-15N,13C-Guanosine,Uridine; 20mM phosphate buffer NA; 100% D2O100% D2O
60.5mM RNA fragment U-15N,13C-Adenosine,Cytidine; 20mM phosphate buffer NA; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 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 DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1collection
VNMR6.1Bcollection
Felix97data analysis
Discover97structure solution
DiscoverBIOSYMrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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