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- PDB-2m58: Structure of 2'-5' AG1 lariat forming ribozyme in its inactive state -

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Basic information

Entry
Database: PDB / ID: 2m58
TitleStructure of 2'-5' AG1 lariat forming ribozyme in its inactive state
ComponentsRNA (59-MER)
KeywordsRNA / lariat / 2'-5' branching
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCarlomagno, T. / Amata, I. / Codutti, L. / Falb, M. / Fohrer, J. / Simon, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme.
Authors: Carlomagno, T. / Amata, I. / Codutti, L. / Falb, M. / Fohrer, J. / Masiewicz, P. / Simon, B.
History
DepositionFeb 18, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2May 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 (59-MER)


Theoretical massNumber of molelcules
Total (without water)19,1631
Polymers19,1631
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (59-MER)


Mass: 19163.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC ribose
1312D 1H-13C HSQC base
1412D HNN-COSY
1512D imino NOESY
1613D HsCNb/HbCNb
1713D (H)CCH-COSY-TOCSY
1813D 13C-edited/ 12C-filtered NOESY
1913D 13C-edited/ 13C-filtered NOESY
11022D 1H-15N HSQC
11122D 1H-13C HSQC ribose
11222D 1H-13C HSQC base
11322D HNN-COSY
11422D imino NOESY
11523D HsCNb/HbCNb
11623D (H)CCH-COSY-TOCSY
11723D 13C-edited/ 12C-filtered NOESY
11823D 13C-edited/ 13C-filtered NOESY
11942D 1H-15N HSQC
12042D 1H-13C HSQC ribose
12142D 1H-13C HSQC base
12242D HNN-COSY
12342D imino NOESY
12443D HsCNb/HbCNb
12543D (H)CCH-COSY-TOCSY
12643D 13C-edited/ 12C-filtered NOESY
12743D 13C-edited/ 13C-filtered NOESY
12832D 1H-15N HSQC
12932D 1H-13C HSQC ribose
13032D 1H-13C HSQC base
13132D HNN-COSY
13232D imino NOESY
13333D HsCNb/HbCNb
13433D (H)CCH-COSY-TOCSY
13533D 13C-edited/ 12C-filtered NOESY
13633D 13C-edited/ 13C-filtered NOESY
13752D 1H-15N HSQC
13852D 1H-13C HSQC ribose
13952D 1H-13C HSQC base
14052D HNN-COSY
14152D imino NOESY
14253D HsCNb/HbCNb
14353D (H)CCH-COSY-TOCSY
14453D 13C-edited/ 12C-filtered NOESY
14553D 13C-edited/ 13C-filtered NOESY
14663D HsCNb/HbCNb
14762D HNN-COSY
14872D imino NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM [U-100% 13C; U-100% 15N] ADENOSINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
2300 uM [U-100% 13C; U-100% 15N] GUANOSINE-5'-MONOPHOSPHATE, 300 uM [U-100% 13C; U-100% 15N] GUANOSINE-5'-TRIPHOSPHATE, 100% D2O100% D2O
3500 uM [U-100% 13C; U-100% 15N] CYTIDINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
4300 uM [U-100% 13C; U-100% 15N] URIDINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
5500 uM [U-100% 13C; U-100% 15N] ADENOSINE-5'-MONOPHOSPHATE, 500 uM [U-100% 13C; U-100% 15N] URIDINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
6500 uM [U-100% 13C; U-100% 15N] ADENOSINE-5'-MONOPHOSPHATE, 500 uM [U-100% 13C; U-100% 15N] URIDINE-5'-MONOPHOSPHATE, 500 uM [U-100% 13C; U-100% 15N] GUANOSINE-5'-MONOPHOSPHATE, 500 uM [U-100% 13C; U-100% 15N] CYTIDINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
7500 uM ADENOSINE-5'-MONOPHOSPHATE, 500 uM URIDINE-5'-MONOPHOSPHATE, 500 uM GUANOSINE-5'-MONOPHOSPHATE, 500 uM CYTIDINE-5'-MONOPHOSPHATE, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMADENOSINE-5'-MONOPHOSPHATE-1[U-100% 13C; U-100% 15N]1
300 uMGUANOSINE-5'-MONOPHOSPHATE-2[U-100% 13C; U-100% 15N]2
300 uMGUANOSINE-5'-TRIPHOSPHATE-3[U-100% 13C; U-100% 15N]2
500 uMCYTIDINE-5'-MONOPHOSPHATE-4[U-100% 13C; U-100% 15N]3
300 uMURIDINE-5'-MONOPHOSPHATE-5[U-100% 13C; U-100% 15N]4
500 uMADENOSINE-5'-MONOPHOSPHATE-6[U-100% 13C; U-100% 15N]5
500 uMURIDINE-5'-MONOPHOSPHATE-7[U-100% 13C; U-100% 15N]5
500 uMADENOSINE-5'-MONOPHOSPHATE-8[U-100% 13C; U-100% 15N]6
500 uMURIDINE-5'-MONOPHOSPHATE-9[U-100% 13C; U-100% 15N]6
500 uMGUANOSINE-5'-MONOPHOSPHATE-10[U-100% 13C; U-100% 15N]6
500 uMCYTIDINE-5'-MONOPHOSPHATE-11[U-100% 13C; U-100% 15N]6
500 uMADENOSINE-5'-MONOPHOSPHATE-127
500 uMURIDINE-5'-MONOPHOSPHATE-137
500 uMGUANOSINE-5'-MONOPHOSPHATE-147
500 uMCYTIDINE-5'-MONOPHOSPHATE-157
Sample conditionsIonic strength: 0.02 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.chemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refined
NMR constraintsNOE constraints total: 1339 / NOE intraresidue total count: 569 / NOE sequential total count: 631
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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