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- PDB-2lk3: U2/U6 Helix I -

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Basic information

Entry
Database: PDB / ID: 2lk3
TitleU2/U6 Helix I
ComponentsRNA (5'-R(*GP*GP*CP*UP*UP*AP*GP*AP*UP*CP*AP*GP*AP*AP*AP*UP*GP*AP*UP*CP*AP*GP*CP*C)-3')
KeywordsRNA / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBurke, J.E. / Sashital, D.G. / Zuo, X.E. / Wang, Y. / Butcher, S.E.
CitationJournal: Rna / Year: 2012
Title: Structure of the yeast U2/U6 snRNA complex.
Authors: Burke, J.E. / Sashital, D.G. / Zuo, X. / Wang, Y.X. / Butcher, S.E.
History
DepositionOct 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7171
Polymers7,7171
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7716.663 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: cell-free synthesis (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D 1H-1H TOCSY
2422D 1H-13C HSQC aromatic
2522D 1H-13C HSQC aliphatic
1632D 1H-15N HMQC
2742D 1H-13C HSQC aromatic
2842D 1H-13C HSQC aliphatic
1952D 1H-15N HMQC
21062D 1H-13C HSQC aromatic
21162D 1H-13C HSQC aliphatic
11232D HNN-COSY
21343D (H)CCH-TOCSY
21443D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.6 mM RNA, 90% H2O/10% D2O90% H2O/10% D2O
20.5-0.6 mM RNA, 100% D2O100% D2O
30.3 mM [U-98% 13C; U-98% 15N] RNA, 90% H2O/10% D2O90% H2O/10% D2O
40.3 mM [U-98% 13C; U-98% 15N] RNA, 100% D2O100% D2O
50.3 mM [U-98% 13C; U-98% 15N] RNA, 17 mg/ml Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
60.3 mM [U-98% 13C; U-98% 15N] RNA, 17 mg/ml Pf1 phage, 100% D2O100% D2O
70.5-0.6 mM RNA, 18 mg/ml Pf1 phage, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA-10.5-0.61
mMRNA-20.5-0.62
0.3 mMRNA-3[U-98% 13C; U-98% 15N]3
0.3 mMRNA-4[U-98% 13C; U-98% 15N]4
0.3 mMRNA-5[U-98% 13C; U-98% 15N]5
17 mg/mLPf1 phage-65
0.3 mMRNA-7[U-98% 13C; U-98% 15N]6
17 mg/mLPf1 phage-86
mMRNA-90.5-0.67
18 mg/mLPf1 phage-107
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
115 7.0 ambient 283 K
215 7.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
VnmrJ1.1Variancollection
NMRPipe97.027.12.56Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 16 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 17 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NA sugar pucker constraints total count: 18 / NOE constraints total: 254 / NOE intraresidue total count: 93 / NOE long range total count: 30 / NOE sequential total count: 131 / Hydrogen bond constraints total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.05 Å / Maximum torsion angle constraint violation: 4.056 ° / Maximum upper distance constraint violation: 0.29 Å
NMR ensemble rmsDistance rms dev: 0.0342 Å / Distance rms dev error: 0.0004 Å

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