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- PDB-2kx8: NMR structure of stem-loop 4 from the human 7SK snRNA in complex ... -

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Basic information

Entry
Database: PDB / ID: 2kx8
TitleNMR structure of stem-loop 4 from the human 7SK snRNA in complex with arginine
Components7SK
KeywordsRNA / snRNA
Function / homologyARGININE / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDurney, M.A. / D'Souza, V.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Preformed protein-binding motifs in 7SK snRNA: structural and thermodynamic comparisons with retroviral TAR.
Authors: Durney, M.A. / D'Souza, V.M.
History
DepositionApr 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 7SK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6242
Polymers13,4491
Non-polymers1751
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 7SK


Mass: 13448.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-13C HSQC
1323D 1H-13C NOESY
1432D 1H-13C HSQC
1533D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 7SK-1, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-13C; U-15N]-Ade/Ura 7SK-AU-2, 100% D2O100% D2O
32 mM [U-13C; U-15N]-Gua/Cyt 7SK-GC-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM7SK-11
2 mM7SK-AU-2[U-13C; U-15N]-Ade/Ura2
2 mM7SK-GC-3[U-13C; U-15N]-Gua/Cyt3
Sample conditionsIonic strength: 0.02 / pH: 5.2 / Pressure: ambient / Temperature: 301 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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