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- PDB-484d: SOLUTION STRUCTURE OF HIV-1 REV PEPTIDE-RNA APTAMER COMPLEX -

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Basic information

Entry
Database: PDB / ID: 484d
TitleSOLUTION STRUCTURE OF HIV-1 REV PEPTIDE-RNA APTAMER COMPLEX
Components
  • BASIC REV PEPTIDE
  • RNA APTAMER
KeywordsRNA BINDING PROTEIN/RNA / HIV-1 REV PEPTIDE / RNA APTAMER / BOUND PEPTIDE SECONDARY STRUCTURE / PEPTIDE- BINDING RNA / TERTIARY ARCHITECTURES / ADAPTIVE-BINDING / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


host cell nucleolus / mRNA transport / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding
Similarity search - Function
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein)
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein Rev / Protein Rev
Similarity search - Component
MethodSOLUTION NMR / DIHEDRAL ANGLE MD
AuthorsYe, X. / Gorin, A.A. / Frederick, R. / Hu, W. / Majumdar, A. / Xu, W. / Mclendon, G. / Ellington, A. / Patel, D.J.
CitationJournal: Chem.Biol. / Year: 1999
Title: RNA architecture dictates the conformations of a bound peptide.
Authors: Ye, X. / Gorin, A. / Frederick, R. / Hu, W. / Majumdar, A. / Xu, W. / McLendon, G. / Ellington, A. / Patel, D.J.
History
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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
B: RNA APTAMER
A: BASIC REV PEPTIDE


Theoretical massNumber of molelcules
Total (without water)11,1462
Polymers11,1462
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)22 / 60LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: RNA chain RNA APTAMER


Mass: 8698.176 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide BASIC REV PEPTIDE


Mass: 2447.819 Da / Num. of mol.: 1 / Fragment: RESIDUES 34-50 / Source method: obtained synthetically
Details: SEQUENCE FROM REV PROTEIN OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
References: UniProt: Q9IQN3, UniProt: Q79994*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE BELOW
NMR detailsText: 2D NOESY (H2O AND D2O), 2D DQ-COSY, 2D TOCSY, 2D 1H-15N HSQC (H2O), 2D 1H-13C HSQC(D2O), 2D 15N-EDITED HMQC-NOESY (H2O), 3D HCCH-COSY (D2O), 3D HCCH-TOCSY ( D2O) AND 3D 13C-EDITED NOESY-HMQC (D2O)

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Sample preparation

DetailsContents: H2O, D2O
Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 6.2 / Pressure: 1 atm / Temperature: 297 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA5001
Varian UNITY INOVAVarianUNITY INOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DIHEDRAL ANGLE MD / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 60 / Conformers submitted total number: 22

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