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- PDB-1mfj: 3' Stem-Loop from Human U4 SNRNA -

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Basic information

Entry
Database: PDB / ID: 1mfj
Title3' Stem-Loop from Human U4 SNRNA
Components5'-R(*GP*AP*CP*AP*GP*UP*CP*UP*CP*UP*AP*CP*GP*GP*AP*GP*AP*CP*UP*G)-3'
KeywordsRNA / RIBONUCLEIC ACID / RNA OLIGONUCLEOTIDE / STEM-AND-LOOP / U4 SMALL NUCLEAR RNA / UACG TETRALOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimization
AuthorsComolli, L.R. / Ulyanov, N.B. / James, T.L. / Gmeiner, W.H.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: NMR Structure of the 3' Stem-Loop from Human U4 snRNA
Authors: Comolli, L.R. / Ulyanov, N.B. / Soto, A.M. / Marky, L.A. / James, T.L. / Gmeiner, W.H.
History
DepositionAug 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 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: 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: 5'-R(*GP*AP*CP*AP*GP*UP*CP*UP*CP*UP*AP*CP*GP*GP*AP*GP*AP*CP*UP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,4231
Polymers6,4231
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 / 15Lowest total energy (a weighted sum of conformational energy and restraint energy).
RepresentativeModel #1lowest total energy

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Components

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


Mass: 6422.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is part of human U4 snRNA.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
131DQF-COSY
1412D TOCSY
151natural abundance 13C-HMQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and complete relaxation matrix analysis of NOE intensities.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chlorideD2O
21 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM sodium phosphate & 50 mM NaCl 6.4ambient 303 K
210 mM sodium phosphate & 50 mM NaCl 6.4ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associates, Inc.collection
NMRPipe2.1Delaglioprocessing
Sparky3Goddard & Knellerdata analysis
MARDIGRAS3.2Borgias et al.iterative matrix relaxation
DYANA1.5Guentertrefinement
miniCarloUlyanov et al.refinement
RefinementMethod: complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimization
Software ordinal: 1
Details: Structures are based on 200 distance restraints, of which 140 are quantitative bounds for nonexchangeable protons calculated with MARDIGRAS, 56 are upper bounds for exchangeable protons, and ...Details: Structures are based on 200 distance restraints, of which 140 are quantitative bounds for nonexchangeable protons calculated with MARDIGRAS, 56 are upper bounds for exchangeable protons, and 4 are hydrogen bond restraints.
NMR representativeSelection criteria: lowest total energy
NMR ensembleConformer selection criteria: Lowest total energy (a weighted sum of conformational energy and restraint energy).
Conformers calculated total number: 15 / Conformers submitted total number: 10

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