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- PDB-2n2o: Structure of murine tumour necrosis factor alpha CDE RNA -

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Basic information

Entry
Database: PDB / ID: 2n2o
TitleStructure of murine tumour necrosis factor alpha CDE RNA
ComponentsRNA (5'-R(P*GP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*UP*U)-3')
KeywordsRNA / CDE / murine / wild type
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCodutti, L. / Leppek, K. / Zalesak, J. / Windeisen, V. / Masiewicz, P. / Stoecklin, G. / Carlomagno, T.
CitationJournal: Structure / Year: 2015
Title: A Distinct, Sequence-Induced Conformation Is Required for Recognition of the Constitutive Decay Element RNA by Roquin.
Authors: Codutti, L. / Leppek, K. / Zalesak, J. / Windeisen, V. / Masiewicz, P. / Stoecklin, G. / Carlomagno, T.
History
DepositionMay 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
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(P*GP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,3431
Polymers7,3431
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7343.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
132immino-1H-1H NOESY
1413D-(H)CCH-COSY-TOCSY
1513D HsCNb/HbCNb
1612D HNN-COSY
1713D 13C-edited NOESY
1812D COSY
1911H-31P HET-COR(P,H-COSY-H,C-HMQC)
1101T1-13C-EDIT relaxation
1111T1rho-13C-EDIT relaxation
112313C-base edited IPAP
113313C-sugar edited IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.30 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 100% D2O100% D2O
20.30 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.30 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 30 mg/mL Pf1 phage, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.30 mMRNA-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
0.30 mMRNA-3[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-42
0.30 mMRNA-5[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate-63
30 mg/mLPf1 phage-73
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
CCPN_Analysis2.3CCPNchemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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