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- PDB-6aas: Solution Structure for helix 45 in 3' end of 12S rRNA -

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Basic information

Entry
Database: PDB / ID: 6aas
TitleSolution Structure for helix 45 in 3' end of 12S rRNA
ComponentsRNA (28-MER)
KeywordsRNA / stem-loop / h45
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, X. / Wu, P.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDPB10,XDB08010101 China
National Natural Science Foundation of China31330018 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.
Authors: Liu, X. / Shen, S. / Wu, P. / Li, F. / Liu, X. / Wang, C. / Gong, Q. / Wu, J. / Yao, X. / Zhang, H. / Shi, Y.
History
DepositionJul 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)9,0351
Polymers9,0351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5280 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (28-MER)


Mass: 9035.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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
111isotropic11H-15N HNN-COSY
121isotropic11H-15N HSQC
131isotropic11H-13C CT-HSQC
141isotropic13D 13C NOESY-HSQC
151isotropic113C (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM helix45, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N]-Ade helix45, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution31 mM [U-13C; U-15N]-Cyt helix45, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution41 mM [U-13C; U-15N]-Gua helix45, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
solution51 mM [U-13C; U-15N]-Ura helix45, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMhelix45natural abundance1
1 mMhelix45[U-13C; U-15N]-Ade2
1 mMhelix45[U-13C; U-15N]-Cyt3
1 mMhelix45[U-13C; U-15N]-Gua4
1 mMhelix45[U-13C; U-15N]-Ura5
Sample conditionsIonic strength: 2 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 160 / Conformers submitted total number: 20

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