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- PDB-2k7e: NMR structure of the human tRNALys3 bound to the HIV genome Loop I -

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Basic information

Entry
Database: PDB / ID: 2k7e
TitleNMR structure of the human tRNALys3 bound to the HIV genome Loop I
Components
  • RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')
  • RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')
KeywordsRNA / tRNALys3 / pseudouridine / HIV / 2-thiouridine / S2U / PSU / modifications
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBilbille, Y. / Vendeix, F.P.A. / Guenther, R. / Malkiewicz, A. / Ariza, X. / Vilarrasa, J. / Agris, P.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs.
Authors: Bilbille, Y. / Vendeix, F.A. / Guenther, R. / Malkiewicz, A. / Ariza, X. / Vilarrasa, J. / Agris, P.F.
History
DepositionAug 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')
B: RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,6432
Polymers7,6432
Non-polymers00
Water0
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 least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')


Mass: 3915.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HIV A-loop
#2: RNA chain RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')


Mass: 3727.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tRNALys3 ASL

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of the human tRNALys3 bound to the HIV genome Loop I containing 2 modified nucleosides: pseudouridine and 2-thiouridine in position 39 and 34 respectively
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H NOESY
2322D 1H-13C HSQC
2422D DQF-COSY
2522D 1H-1H NOESY
1612D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), 0.3 mM T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM RNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3'), 0.3 mM T-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.3 mMRNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')1
0.3 mMT-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')1
10 mMsodium phosphate1
100 mMsodium chloride1
0.3 mMRNA (5'-R(*GP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*G)-3')2
0.3 mMT-RNA (5'-R(*CP*UP*(SUR)P*UP*UP*AP*AP*(PSU)P*CP*UP*GP*C)-3')2
10 mMsodium phosphate2
100 mMsodium chloride2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.5 ambient 276 K
20.1 6.5 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddardchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
XwinNMRBruker Biospincollection
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 292 / NOE intraresidue total count: 115 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 139
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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