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- PDB-1u2a: STEM LOOP IIA FROM U2SNRNA OF SACCHAROMYCES CEREVISIAE, NMR, MINI... -

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Basic information

Entry
Database: PDB / ID: 1u2a
TitleSTEM LOOP IIA FROM U2SNRNA OF SACCHAROMYCES CEREVISIAE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRNA (5'-R(P*GP*GP*UP*CP*AP*GP*UP*GP*UP*AP*AP*CP*AP*AP*CP*UP*GP*AP*CP*C)-3')
KeywordsRNA / PRE-MRNA SPLICING / U2SNRNA / U-TURN / RNA-PROTEIN INTERACTIONS / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
AuthorsStallings, S.C. / Moore, P.B.
Citation
Journal: Structure / Year: 1997
Title: The structure of an essential splicing element: stem loop IIa from yeast U2 snRNA.
Authors: Stallings, S.C. / Moore, P.B.
#1: Journal: Genes Dev. / Year: 1991
Title: Efficient Association of U2 Snrnps with Pre-Mrna Requires an Essential U2 RNA Structural Element
Authors: Zavanelli, M.I. / Ares Junior, M.
#2: Journal: Genes Dev. / Year: 1990
Title: Lethal and Temperature-Sensitive Mutations and Their Suppressors Identify an Essential Structural Element in U2 Small Nuclear RNA
Authors: Ares Junior, M. / Igel, A.H.
History
DepositionAug 19, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: RNA (5'-R(P*GP*GP*UP*CP*AP*GP*UP*GP*UP*AP*AP*CP*AP*AP*CP*UP*GP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,4071
Polymers6,4071
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 / 15NOE VIOLATIONS < 0.2A (NOT APPLIED TO PSEUDO-NOES IN THE TERMINAL BASE PAIR), DIHEDRAL VIOL < 2 DEGREES, RMSD BONDS < 0.02A, RMSD ANGLE < 2 DEGREES, RMSD IMPROPER < 2 DEGREES
Representative

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Components

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


Mass: 6406.878 Da / Num. of mol.: 1 / Fragment: STEM LOOP IIA
Mutation: TWO TERMINAL BASE PAIRS WERE CHANGED FROM UAS IN STEM LOOP IIA TO GCS IN U2A TO ACCOMMODATE T7 TRANSCRIPTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: MOLECULE TRANSCRIBED FROM A PARTIALLY SINGLE-STRANDED DNA TEMPLATE USING T7 RNA POLYMERASE
Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY(D2O)
121NOESY(H2O)
131DQF-COSY
141HP-COSY
151SPIN-ECHO DIFFERENCE-HMQC
1613D (H)CCH-TOCSY
1713D (H)CCH-TOCSY

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Sample preparation

Sample conditionsIonic strength: 75 mM / pH: 7.6
Pressure: 1 ATM SOLVENT SYSTEM : 10MM KH2PO4, 50 MM KCL, 15 MM NACL, 0.5 MM UREA atm
Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGA500GEOMEGA5005001
Varian UNITY+600VarianUNITY+6006002

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
FELIX95structure solution
XPLOR3.851structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: REFINEMENT WAS DONE USING TORSION ANGLE MOLECULAR DYNAMICS. DETAILS OF THE PROTOCOL CAN BE FOUND IN THE STRUCTURE CITATION ABOVE.
NMR ensembleConformer selection criteria: NOE VIOLATIONS < 0.2A (NOT APPLIED TO PSEUDO-NOES IN THE TERMINAL BASE PAIR), DIHEDRAL VIOL < 2 DEGREES, RMSD BONDS < 0.02A, RMSD ANGLE < 2 DEGREES, RMSD IMPROPER < 2 DEGREES
Conformers calculated total number: 15 / Conformers submitted total number: 1

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