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- PDB-5iem: NMR structure of the 5'-terminal hairpin of the 7SK snRNA -

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Basic information

Entry
Database: PDB / ID: 5iem
TitleNMR structure of the 5'-terminal hairpin of the 7SK snRNA
Components7SK snRNA
KeywordsTRANSCRIPTION / RNA / regulator
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBourbigot, S. / Dock-Bregeon, A.C. / Coutant, J. / Kieffer, B. / Lebars, I.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-2010-JCJC-1507-01 France
CitationJournal: RNA / Year: 2016
Title: Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA.
Authors: Bourbigot, S. / Dock-Bregeon, A.C. / Eberling, P. / Coutant, J. / Kieffer, B. / Lebars, I.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / Item: _citation.journal_abbrev / _entity.pdbx_description
Revision 1.4Jun 6, 2018Group: Data collection / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_ensemble ...pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_representative
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number
Revision 1.5Jun 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: 7SK snRNA


Theoretical massNumber of molelcules
Total (without water)18,2691
Polymers18,2691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations,lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: RNA chain 7SK snRNA


Mass: 18268.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA / 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
111isotropic22D 1H-1H NOESY
121isotropic22D 1H-15N HSQC
232isotropic22D 1H-1H NOESY
242isotropic22D 1H-13C HSQC
353anisotropic22D 1H-13C HSQC
262isotropic32D 1H-1H TOCSY
272isotropic22D DQF-COSY
282isotropic23D (H)CCH-TOCSY
393anisotropic22D 1H-15N HSQC
2102isotropic13D HCP
2112isotropic12D HPCOSY
2122isotropic22D HCN

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-99% 13C; U-99% 15N] HPI, 90% H2O/10% D2OHPI90% H2O/10% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] HPI, 100% D2OHPI100% D2O
filamentous virus30.4 mM [U-99% 13C; U-99% 15N] HPI, 90% H2O/10% D2OHPI90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMHPI[U-99% 13C; U-99% 15N]1
0.4 mMHPI[U-99% 13C; U-99% 15N]2
0.4 mMHPI[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1sodium phosphate buffer50 mMconditions_16.4 ambient Pa288 K
2sodium phosphate buffer50 mMconditions_26.4 ambient Pa303 K
3sodium phosphate buffer50 mMconditions_36.4 ambient Pa303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker DRXBrukerDRX6003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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