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- PDB-5n5c: NMR solution structure of the TSL2 RNA hairpin -

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Basic information

Entry
Database: PDB / ID: 5n5c
TitleNMR solution structure of the TSL2 RNA hairpin
ComponentsRNA (19-MER)
KeywordsRNA / Terminal Stem-Loop 2 Survival Motor Neuron
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsGarcia-Lopez, A. / Wacker, A. / Tessaro, F. / Jonker, H.R.A. / Richter, C. / Comte, A. / Berntenis, N. / Schmucki, R. / Hatje, K. / Sciarra, D. ...Garcia-Lopez, A. / Wacker, A. / Tessaro, F. / Jonker, H.R.A. / Richter, C. / Comte, A. / Berntenis, N. / Schmucki, R. / Hatje, K. / Sciarra, D. / Konieczny, P. / Fournet, G. / Faustino, I. / Orozco, M. / Artero, R. / Goekjian, P. / Metzger, F. / Ebeling, M. / Joseph, B. / Schwalbe, H. / Scapozza, L.
Funding support Germany, Switzerland, Spain, 9items
OrganizationGrant numberCountry
European Union261863
iNEXT - European Union Horizon 2020 programme653706
European Union261572
LOEWE program SynChemBio Germany
German Research Foundation Germany
European Molecular Biology OrganizationALTF 253-2012
SMA Europe17623 and 19243
Schmidheiny Foundation Switzerland
Generalitat Valenciana - Santiago Grisolia PhD program Spain
CitationJournal: Nat Commun / Year: 2018
Title: Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes.
Authors: Garcia-Lopez, A. / Tessaro, F. / Jonker, H.R.A. / Wacker, A. / Richter, C. / Comte, A. / Berntenis, N. / Schmucki, R. / Hatje, K. / Petermann, O. / Chiriano, G. / Perozzo, R. / Sciarra, D. / ...Authors: Garcia-Lopez, A. / Tessaro, F. / Jonker, H.R.A. / Wacker, A. / Richter, C. / Comte, A. / Berntenis, N. / Schmucki, R. / Hatje, K. / Petermann, O. / Chiriano, G. / Perozzo, R. / Sciarra, D. / Konieczny, P. / Faustino, I. / Fournet, G. / Orozco, M. / Artero, R. / Metzger, F. / Ebeling, M. / Goekjian, P. / Joseph, B. / Schwalbe, H. / Scapozza, L.
History
DepositionFeb 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (19-MER)


Theoretical massNumber of molelcules
Total (without water)6,0491
Polymers6,0491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3780 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (19-MER)


Mass: 6048.626 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
112isotropic32D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
231isotropic32D 1H-1H NOESY
143isotropic23D 1H-13C NOESY
153isotropic32D 12C-filtered 1H-1H NOESY
163isotropic32D 13C-editted 1H-1H NOESY
172isotropic32D 1H-1H TOCSY
182isotropic32D 1H-1H COSY
192isotropic32D 1H-13C HSQC
1103isotropic32D 1H-13C HSQC aromatic
1113isotropic32D 1H-13C HSQC sugar
1121isotropic32D 1H-15N HSQC
1133isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2OH2O90% H2O/10% D2O
solution20.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2OD2O99.8% D2O
solution30.6 mM [U-98% 13C; U-96-98% 15N]-ADE RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2OADE99.8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRNA (19-MER)natural abundance1
50 mMsodium phosphatenatural abundance1
0.1 mMEDTAnatural abundance1
0.6 mMRNA (19-MER)natural abundance2
50 mMsodium phosphatenatural abundance2
0.1 mMEDTAnatural abundance2
0.6 mMRNA (19-MER)[U-98% 13C; U-96-98% 15N]-ADE3
50 mMsodium phosphatenatural abundance3
0.1 mMEDTAnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
174 mM298K6.4 ambient mbar298 K
271 mM278K6.4 ambient mbar278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryoprobe
Bruker AVANCEBrukerAVANCE8002cryoprobe
Bruker AVANCEBrukerAVANCE9003cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpinBruker Biospinprocessing
Sparky3.114Kneller and Goddardchemical shift assignment
Sparky3.114Kneller and Goddardpeak picking
Sparky3.114Kneller and Goddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2 HJ development versionLinge, O'Donoghue and Nilgesrefinement
ARIA1.2 HJ development versionLinge, O'Donoghue and Nilgesrefinement
Refinement
MethodSoftware ordinalDetails
simulated annealing7cartesian angle dynamics
molecular dynamics8refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 40

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