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- PDB-2mqt: Solution NMR structure of the U5-primer binding site (U5-PBS) dom... -

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Basic information

Entry
Database: PDB / ID: 2mqt
TitleSolution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome
ComponentsRNA (68-MER)
KeywordsRNA / U5-primer binding site / U5-PBS / YNMG tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesMurine Leukemia Virus
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsD'Souza, V. / Yildiz, Z.
CitationJournal: Nature / Year: 2014
Title: A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing.
Authors: Miller, S.B. / Yildiz, F.Z. / Lo, J.A. / Wang, B. / D'Souza, V.M.
History
DepositionJun 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (68-MER)


Theoretical massNumber of molelcules
Total (without water)21,8941
Polymers21,8941
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 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (68-MER)


Mass: 21893.887 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: in vitro transcription by T7 polymerase using pUC19 vector
Source: (synth.) Murine Leukemia Virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC
1512D 1H-1H NOESYin H2O
1612D 1H-1H NOESYin D2O
1713D 1H-13C NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY
11013D 1H-13C NOESY
11112D 1H-15N HSQC
11212D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] U5-PBS, 100% D2O / Solvent system: 100% D2O
SampleConc.: 0.8 mM / Component: U5-PBS-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 10mM Tris, 10mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 311 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANACase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
CYANACase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
CYANACase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAJohnson, One Moon Scientificstructure solution
CYANAJohnson, One Moon Scientificdata analysis
CYANAJohnson, One Moon Scientificprocessing
Amberrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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