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- PDB-2kry: Solution structure of the human mitochondrial tRNAMet ASL contain... -

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Basic information

Entry
Database: PDB / ID: 2kry
TitleSolution structure of the human mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34
ComponentsRNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')
KeywordsRNA / tRNA / 5-formylcytidine / ASL / modification
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBilbille, Y. / Agris, P.F.
CitationJournal: To be Published
Title: The Human Mitochondrial tRNAMet ASL structure solved by Nuclear Magnetic Resonance
Authors: Bilbille, Y. / Harris, K. / Agris, P.F.
History
DepositionDec 23, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 17, 2016Group: Non-polymer description
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,4051
Polymers5,4051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')


Mass: 5405.279 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D DQF-COSY
1412D 1H-1H COSY
1512D 1H-1H TOCSY
1622D 1H-13C HSQC
1722D 1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMRNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-11
1 mMRNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-22
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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