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

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Basic information

Entry
Database: PDB / ID: 6xxa
TitleConstitutive decay element CDE2 from human 3'UTR
ComponentsCDE2
KeywordsRNA / hairpin Roquin binding
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesThermosinus carboxydivorans Nor1 (bacteria)
MethodSOLUTION NMR / simulated annealing
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 27, 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: CDE2


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 area4280 Å2
MethodPISA
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 CDE2


Mass: 6690.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermosinus carboxydivorans Nor1 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic42D 1H-1H NOESY
121isotropic22D 1H-13C HSQC
232isotropic32D gamma HCN
242isotropic13D HCN
252isotropic1fwHCCH-TOCSY-CCH-E.COSY
262isotropic13D HCP
272isotropic12D qHCP
282isotropic1(H)CCH-TOCSY
292isotropic52D PFIDS

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1900 uM CDE2, 100% D2O25 mM potassium phosphate buffer 50 mM KCld2o_nat_ab100% D2O
solution21300 uM [U-99% 13C; U-99% 15N] CDE2, 100% D2O25 mM potassium phosphate buffer 50 mM KCld2o_13c15n100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
900 uMCDE2natural abundance1
1300 uMCDE2[U-99% 13C; U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
125 mM potassium phosphate, 50 mM KCl Not definedd2o_natab6.2 1 bar298 K
225 mM potassium phosphate, 50 mM KCl Not definedd2o_13c15n6.2 1 bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III9003
Bruker AVANCE IIIBrukerAVANCE III9504
Bruker AVANCE IIIBrukerAVANCE III7005

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.structure calculation
Sparky3.2Goddardpeak picking
Sparky3.2Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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