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- PDB-2mfd: The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Ent... -

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Basic information

Entry
Database: PDB / ID: 2mfd
TitleThe Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03
Components5'-R(P*GP*GP*CP*GP*UP*UP*CP*GP*CP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3'
KeywordsRNA / 5'-NTR / cloverleaf
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBovine enterovirus type 1
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailsclosest to the average, model1
AuthorsIhle, Y. / Zell, R. / Gorlach, M.
CitationJournal: To be Published
Title: The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir 404/03
Authors: Ihle, Y. / Zell, R. / Gorlach, M.
History
DepositionOct 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_software.name / _pdbx_nmr_spectrometer.model
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: 5'-R(P*GP*GP*CP*GP*UP*UP*CP*GP*CP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0711
Polymers6,0711
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)20 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 6070.633 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Bovine enterovirus type 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC aliphatic
1212D 1H-13C HSQC aromatic
1312D 1H-1H COSY
1412D 1H-1H NOESY
1512D DQF-COSY
1612D 1H-1H TOCSY
1722D HcncH + 2D (H)CCH-COSY
1822D HcnH + 2D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aromatic
21212D 1H-1H NOESY
21322D 1H-13C HSQC aliphatic
21422D 1H-13C HSQC aromatic
21512D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM BEVSLD5, 10 mM potassium phosphate, 40 mM potassium chloride, 0.2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-100% 13C; U-100% 15N] BEVSLD5, 10 mM potassium phosphate, 40 mM potassium chloride, 0.2 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMBEVSLD5-11
10 mMpotassium phosphate-21
40 mMpotassium chloride-31
0.2 mMEDTA-41
0.9 mMBEVSLD5-5[U-100% 13C; U-100% 15N]2
10 mMpotassium phosphate-62
40 mMpotassium chloride-72
0.2 mMEDTA-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1506.2ambient 293 K
2506.2ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.5.5Rochus Kellerchemical shift assignment
CARA1.5.5Rochus Kellerpeak picking
CYANA1.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1 / Details: refinement in water based on ARIA scripts
NMR constraintsNA alpha-angle constraints total count: 18 / NA beta-angle constraints total count: 18 / NA chi-angle constraints total count: 19 / NA delta-angle constraints total count: 19 / NA epsilon-angle constraints total count: 18 / NA gamma-angle constraints total count: 19 / NA other-angle constraints total count: 18 / NA sugar pucker constraints total count: 19 / NOE constraints total: 587 / NOE intraresidue total count: 268 / NOE long range total count: 59 / NOE medium range total count: 17 / NOE sequential total count: 243 / Hydrogen bond constraints total count: 36
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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