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- PDB-2m1a: HIV-1 Rev ARM peptide (residues T34-R50) -

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Basic information

Entry
Database: PDB / ID: 2m1a
TitleHIV-1 Rev ARM peptide (residues T34-R50)
ComponentsHIV-1 Rev arginine-rich motif (ARM)
KeywordsVIRAL PROTEIN / HIV / Rev / arginine-rich motif
Function / homologyAnti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / host cell nucleolus / mRNA transport / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding / Protein Rev
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / torsion angle dynamics, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 1
AuthorsCasu, F. / Duggan, B.M. / Hennig, M.
CitationJournal: Biophys.J. / Year: 2013
Title: The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding.
Authors: Casu, F. / Duggan, B.M. / Hennig, M.
History
DepositionNov 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HIV-1 Rev arginine-rich motif (ARM)


Theoretical massNumber of molelcules
Total (without water)3,2201
Polymers3,2201
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HIV-1 Rev arginine-rich motif (ARM)


Mass: 3219.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Description: Expression controlled with the T7 lac promoter / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: G3C324*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The data presented are for the Rev arginine-rich motif (ARM), which comprises native residues 34-50 of the HIV-1 Rev protein and constitutes the protein RNA-binding domain and nuclear import ...Details: The data presented are for the Rev arginine-rich motif (ARM), which comprises native residues 34-50 of the HIV-1 Rev protein and constitutes the protein RNA-binding domain and nuclear import signal. This NMR structure was solved in a 50% TFE/aqueous buffer mixture.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC NH2 only
1322D 1H-13C HSQC
1423D HNCO
1523D HNCA
1623D HN(CO)CA
1723D CBCA(CO)NH
1823D HN(CA)CB
1923D HBHA(CO)NH
11023D H(CCO)NH
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11323D (H)CCH-TOCSY
11413D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-15N] Rev ARM peptide, 50 mM sodium phosphate, 150 mM potassium chloride, 1 mM EDTA, 1 mM DTT, 0.02 % sodium azide, 10.0 % [U-99% 2H] D2O, 40.0 % H2O, 50.0 % TFE, trifluoroethanol/watertrifluoroethanol/water
21.0 mM [U-13C; U-15N] Rev ARM peptide, 50 mM sodium phosphate, 150 mM potassium chloride, 1 mM EDTA, 1 mM DTT, 0.02 % sodium azide, 10.0 % [U-99% 2H] D2O, 40.0 % H2O, 50.0 % [U-99% 2H] TFE, trifluoroethanol/watertrifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRev ARM peptide-1[U-15N]1
50 mMsodium phosphate-21
150 mMpotassium chloride-31
1 mMEDTA-41
1 mMDTT-51
0.02 %sodium azide-61
10.0 %D2O-7[U-99% 2H]1
40.0 %H2O-81
50.0 %TFE-91
1.0 mMRev ARM peptide-10[U-13C; U-15N]2
50 mMsodium phosphate-112
150 mMpotassium chloride-122
1 mMEDTA-132
1 mMDTT-142
0.02 %sodium azide-152
10.0 %D2O-16[U-99% 2H]2
40.0 %H2O-172
50.0 %TFE-18[U-99% 2H]2
Sample conditionspH: 7.4 / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, TORSION ANGLE DYNAMICS / Software ordinal: 1
NMR constraintsNOE constraints total: 236 / NOE intraresidue total count: 118 / NOE long range total count: 0 / NOE medium range total count: 53 / NOE sequential total count: 65 / Protein phi angle constraints total count: 24 / Protein psi angle constraints total count: 24
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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