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- PDB-1lmv: Solution structure of the unmodified U2 snRNA-intron branch site ... -

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Basic information

Entry
Database: PDB / ID: 1lmv
TitleSolution structure of the unmodified U2 snRNA-intron branch site helix from S. cerevisiae
Components
  • 5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3'
  • 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'
KeywordsRNA / U2 snRNA / branch site / solution structure / A-form helix
Function / homologyRNA
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle molecular dynamics, congugate gradient minimization
AuthorsNewby, M.I. / Greenbaum, N.L.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine
Authors: Newby, M.I. / Greenbaum, N.L.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 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
Remark 999SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds ...SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds to position 5 on strand A, which is a uridine in 1LMV, and a pseudouridine in 1LPW.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3'
B: 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0182
Polymers6,0182
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)10 / 300structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3'


Mass: 2912.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: unmodified U2 snRNA. Region of U2 snRNA that pairs with the intron branch site during spliceosome assembly (nucleotides 34-39 in yeast U2 snRNA).
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#2: RNA chain 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'


Mass: 3104.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Intron branch site sequence. Region of the pre-mRNA intron that contains the conserved branch site sequence, and pairs with U2 snRNA during spliceosome assembly.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
242DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times to assess the buildup rate of each NOE, thereby resolving ...Text: This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times to assess the buildup rate of each NOE, thereby resolving some of the spectral overlap.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA90% H2O/10% D2O
21mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM sodium chloride 6.4 ambient 278 K
250mM sodium chloride 6.4 ambient 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 spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 720 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3Varian, Inc.collection
Sparky3.69T.D. Goddard and D.G. Knellerdata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle molecular dynamics, congugate gradient minimization
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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