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- PDB-1i9f: STRUCTURAL CHARACTERIZATION OF THE COMPLEX OF THE REV RESPONSE EL... -

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Basic information

Entry
Database: PDB / ID: 1i9f
TitleSTRUCTURAL CHARACTERIZATION OF THE COMPLEX OF THE REV RESPONSE ELEMENT RNA WITH A SELECTED PEPTIDE
Components
  • REV RESPONSE ELEMENT RNA
  • RSG-1.2 PEPTIDE
KeywordsDE-NOVO PROTEIN/RNA / peptide-RNA complex / RNA recognition / selected peptide / solution structure / DE-NOVO PROTEIN-RNA COMPLEX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsZhang, Q. / Harada, K. / Cho, H.S. / Frankel, A. / Wemmer, D.E.
CitationJournal: Chem.Biol. / Year: 2001
Title: Structural characterization of the complex of the Rev response element RNA with a selected peptide.
Authors: Zhang, Q. / Harada, K. / Cho, H.S. / Frankel, A.D. / Wemmer, D.E.
History
DepositionMar 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REV RESPONSE ELEMENT RNA
B: RSG-1.2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,1852
Polymers13,1852
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)7 / 20
Representativefewest violations, lowest energy

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Components

#1: RNA chain REV RESPONSE ELEMENT RNA / RRE / HIV-1 RRE RNA


Mass: 11039.639 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence naturally occurs in HUMAN IMMUNODEFICIENCY VIRUS TYPE 1, strain DH5a
#2: Protein/peptide RSG-1.2 PEPTIDE


Mass: 2145.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 19-MER PEPTIDE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141DQF-COSY
151HNCA-J

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Sample preparation

DetailsContents: 1.6 mM RNA/peptide
Solvent system: 90% H2O/10% D2O, 20 mM sodium phosphate, 100 mM sodium chloride, 0.1 mM EDTA, pH 6.5
Sample conditionsIonic strength: 20mM sodium phosphate, 100 mM sodium chloride
pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
Field strength (MHz)Spectrometer-ID
5001
6002

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Processing

NMR software
NameClassification
XEASYdata analysis
Felixdata analysis
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 7

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