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- PDB-1ull: RNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ull
TitleRNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 STRUCTURES
Components
  • REV PEPTIDE
  • RNA (5'-R (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP*CP*UP*UP*CP*GP* GP*UP*AP*CP*UP*GP*GP*AP*GP*AP*AP*AP*CP*AP*GP*CP*C)-3')
KeywordsViral protein/RNA / REV PEPTIDE-RNA RECOGNITION / ALPHA-HELIX IN WIDENED RNA MAJOR GROOVE / PURINE-PURINE MISMATCHES / UAU BASE TRIPLE / ADAPTIVE BINDING OF PEPTIDE AND RNA IN COMPLEX / COMPLEX (RNA APTAMER-REV PEPTIDE) / Viral 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsYe, X. / Gorin, A. / Ellington, A.D. / Patel, D.J.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex.
Authors: Ye, X. / Gorin, A. / Ellington, A.D. / Patel, D.J.
History
DepositionNov 5, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP*CP*UP*UP*CP*GP* GP*UP*AP*CP*UP*GP*GP*AP*GP*AP*AP*AP*CP*AP*GP*CP*C)-3')
B: REV PEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,7242
Polymers13,7242
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 / 14ENERGY GAP 400 KCAL/MOLE
Representative

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Components

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


Mass: 11275.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 17-MER PEPTIDE OF REV PROTEIN FROM HIV-I
#2: Protein/peptide REV PEPTIDE


Mass: 2447.819 Da / Num. of mol.: 1 / Fragment: RESIDUES 34 - 50
Source method: isolated from a genetically manipulated source
Details: REV PEPTIDE / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P05866

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 297 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VARIAN VNMR (2D) NMRPIPE (3D) PIPP (3D)(3D)structure solution
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY GAP 400 KCAL/MOLE / Conformers calculated total number: 14 / Conformers submitted total number: 7

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