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- PDB-6mxq: Solution structure of a c-JUN 5' UTR stem-loop associated with sp... -

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Basic information

Entry
Database: PDB / ID: 6mxq
TitleSolution structure of a c-JUN 5' UTR stem-loop associated with specialized cap-dependent translation initiation
ComponentsRNA C-JUN TL
KeywordsRNA / c-JUN / mRNA / eIF3 / cap-dependent / specialized translation initiation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWalker, M. / Shortridge, M. / Varani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)62-8160 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structure of the RNA Specialized Translation Initiation Element that Recruits eIF3 to the 5'-UTR of c-Jun.
Authors: Walker, M.J. / Shortridge, M.D. / Albin, D.D. / Cominsky, L.Y. / Varani, G.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2May 1, 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 C-JUN TL


Theoretical massNumber of molelcules
Total (without water)15,5231
Polymers15,5231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA C-JUN TL


Mass: 15523.181 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
111isotropic12D 1H-1H NOESY
222isotropic12D 1H-1H NOESY
133isotropic12D 1H-1H NOESY
144isotropic13D 1H-13C NOESY
255isotropic22D 1H-15N HSQC
164isotropic12D 1H-13C HSQC
171isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM RNA, 100% D2OTL-1100% D2O
solution21.0 mM RNA, 90% H2O/10% D2OTL-290% H2O/10% D2O
solution31.0 mM [A,G-98% D3',4',5',5"; C,U-98%: D3',4',5, 5',5"] RNA, 100% D2OTL-3100% D2O
solution41.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA, 100% D2OTL-4100% D2O
solution51.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA, 90% H2O/10% D2OTL-590% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRNAnatural abundance1
1.0 mMRNAnatural abundance2
1.0 mMRNA[A,G-98% D3',4',5',5"; C,U-98%: D3',4',5, 5',5"]3
1.0 mMRNA[A,C,G,U-98% 13C, A,C,G,U-98% 15N]4
1.0 mMRNA[A,C,G,U-98% 13C, A,C,G,U-98% 15N]5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120mM Sodium Phosphate Not definedconditions-16.1 1 atm298 K
220mM Sodium Phosphate Not definedconditions-26.1 1 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIBrukerAVANCE II6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CcpNmr AnalysisCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TopSpinBruker Biospinchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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