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- PDB-6xwj: Constitutive decay element CDE2 from human 3'UTR -

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Basic information

Entry
Database: PDB / ID: 6xwj
TitleConstitutive decay element CDE2 from human 3'UTR
ComponentsRNA (5'-R(*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*C)-3')
KeywordsRNA / hairpin Roquin binding
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsSchwalbe, H. / Binas, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis for the recognition of transiently structured AU-rich elements by Roquin.
Authors: Binas, O. / Tants, J.N. / Peter, S.A. / Janowski, R. / Davydova, E. / Braun, J. / Niessing, D. / Schwalbe, H. / Weigand, J.E. / Schlundt, A.
History
DepositionJan 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,6901
Polymers6,6901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4000 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6690.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-1H NOESY
222isotropic13D (H)CCH-TOCSY
232isotropic1gamma HCN
242isotropic1fwHCC-TOCSY-CCH-E.COSY
252isotropic13D HCP
262isotropic22D PFIDS
272isotropic13D HCP-TOCSY
181isotropic12D 1H-13C HSQC
292isotropic13D HCN

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM CDE2, 100% D2O25 mM potassium phosphate buffer, pH 6.2, 50 mM KCld2o_unlabeled100% D2O
solution21300 uM [U-99% 13C; U-99% 15N] CDE2, 100% D2O25 mM potassium phosphate buffer, pH 6.2, 50 mM KCld2o_13c15n100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMCDE2natural abundance1
1300 uMCDE2[U-99% 13C; U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM KCl 25 mM potassium phosphate buffer Not definedd2o_unlabeled_conditions6.2 1 bar298 K
250 mM KCl 25 mM potassium phosphate buffer Not definedd2o_13c15n_conditions6.2 1 bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III9503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.structure calculation
X-PLOR NIH2.52Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3Goddardchemical shift assignment
Sparky3Goddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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