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- PDB-2n3r: NMR structure of the II-III-VI three-way junction from the VS rib... -

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Basic information

Entry
Database: PDB / ID: 2n3r
TitleNMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
ComponentsRNA (62-MER)
KeywordsRNA / VS ribozyme / Catalysis / Mg2+ ions
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsBonneau, E. / Girard, N. / Lemieux, S. / Legault, P.
CitationJournal: Rna / Year: 2015
Title: The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.
Authors: Bonneau, E. / Girard, N. / Lemieux, S. / Legault, P.
History
DepositionJun 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2May 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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (62-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2169
Polymers20,0221
Non-polymers1948
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 500structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (62-MER)


Mass: 20021.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 1H WATERGATE
1212D 1H-15N HSQC
1312D 1H-15N HSQC NH2 only
1412D HNN COSY
1512D 1H-1H NOESY
1612D 1H-15N CPMG-NOESY
1713D 15N-edited NOESY-HSQC
1863D 15N/13C-edited NOESY-HSQC
1962D G-specific H(NC)-TOCSY-(C)H
11062D A-specific H(NC)-TOCSY-(C)H
21122D 1H-15N MQ-(HC)N(C)H
21222D 1H-13C HSQC
21322D 1H-13C HMQC
21423D (H)CCH-COSY
21523D (H)CCH-TOCSY
21623D 13C-edited NOESY-HSQC
21732D 1H-13C HSQC
21832D 1H-13C HMQC
21933D (H)CCH-COSY
22033D (H)CCH-TOCSY
22133D 13C-edited NOESY-HSQC
22242D 1H-13C HSQC
22342D 1H-13C HMQC
22443D (H)CCH-COSY
22543D (H)CCH-TOCSY
22643D 13C-edited NOESY-HSQC
22752D 1H-13C HSQC
22852D 1H-13C HMQC
22953D (H)CCH-COSY
23053D (H)CCH-TOCSY
23153D 13C-edited NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-15N] RNA (62-MER), 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-13C; U-15N] RNA (62-MER), 100% D2O100% D2O
32 mM [U-13C; U-15N]-Ade RNA (62-MER), 100% D2O100% D2O
42 mM [U-13C; U-15N]-Cyt RNA (62-MER), 100% D2O100% D2O
52.5 mM [U-13C; U-15N]-Gua RNA (62-MER), 100% D2O100% D2O
62 mM [U-13C; U-15N] RNA (62-MER), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRNA (62-MER)-1[U-15N]1
2 mMRNA (62-MER)-2[U-13C; U-15N]2
2 mMRNA (62-MER)-3[U-13C; U-15N]-Ade3
2 mMRNA (62-MER)-4[U-13C; U-15N]-Cyt4
2.5 mMRNA (62-MER)-5[U-13C; U-15N]-Gua5
2 mMRNA (62-MER)-6[U-13C; U-15N]6
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 288 K
26.5 ambient 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CCPNMRCCPNdata analysis
CCPNMRCCPNchemical shift assignment
CCPNMRCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 21

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