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- PDB-1g70: COMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1g70
TitleCOMPLEX OF HIV-1 RRE-IIB RNA WITH RSG-1.2 PEPTIDE
Components
  • HIV-1 RRE-IIB 32 NUCLEOTIDE RNA
  • RSG-1.2 PEPTIDE
KeywordsVIRAL PROTEIN/RNA / peptide-RNA complex / non-canonical base pairs / VIRAL PROTEIN-RNA COMPLEX
Function / homologyRNA / RNA (> 10) / :
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsGosser, Y. / Hermann, T. / Majumdar, A. / Hu, W. / Frederick, R. / Jiang, F. / Xu, W. / Patel, D.J.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Peptide-triggered conformational switch in HIV-1 RRE RNA complexes.
Authors: Gosser, Y. / Hermann, T. / Majumdar, A. / Hu, W. / Frederick, R. / Jiang, F. / Xu, W. / Patel, D.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Molding a peptide into an RNA site by in vivo peptide evolution
Authors: Harada, K. / Martin, S.S. / Tan, R. / Frankel, A.D.
#2: Journal: Science / Year: 1996
Title: alpha Helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex
Authors: Battiste, J.L. / Mao, H. / Rao, N.S. / Tan, R. / Muhandiram, D.R. / Kay, L.E. / Frankel, A.D. / Williamson, J.R.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 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: HIV-1 RRE-IIB 32 NUCLEOTIDE RNA
B: RSG-1.2 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,9182
Polymers12,9182
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 90structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1

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Components

#1: RNA chain HIV-1 RRE-IIB 32 NUCLEOTIDE RNA


Mass: 10343.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: T7 IN VITRO TRANSCRIPTION
#2: Protein/peptide RSG-1.2 PEPTIDE


Mass: 2574.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: IN VIVO-SELECTED PEPTIDE / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D homonuclear experiments, 2D, 3D heteronuclear experiments

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Sample preparation

Sample conditionsIonic strength: 10mM Sodium phosphate, 12.5mM Sodium acetate, 25mM Sodium chloride, 0.1mM EDTA
pH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio, F., et al.processing
NMRView2.1.2Johnson, B.A., Blevins, R.A.data analysis
Amber4.1Kollman, P., et al.structure solution
Amber4.1Kollman, P., et al.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 14

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