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- PDB-2kmj: High resolution NMR solution structure of a complex of HIV-2 TAR ... -

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Basic information

Entry
Database: PDB / ID: 2kmj
TitleHigh resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry
Components
  • Pyrimidinylpeptide
  • RNA (28-MER)
KeywordsRNA/PEPTIDE / RNA-ligand complex / binding stoichiometry / HIV-2 TAR / RNA-PEPTIDE COMPLEX
Function / homologypolypeptide(D) / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 2
MethodSOLUTION NMR / simulated annealing
Model detailsTop-ranked ensemble, model 1
AuthorsFerner, J. / Suhartono, M. / Breitung, S. / Jonker, H.R.A. / Hennig, M. / Woehnert, J. / Goebel, M. / Schwalbe, H.
CitationJournal: Chembiochem / Year: 2009
Title: Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries.
Authors: Ferner, J. / Suhartono, M. / Breitung, S. / Jonker, H.R.A. / Hennig, M. / Wohnert, J. / Gobel, M. / Schwalbe, H.
History
DepositionJul 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_end
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (28-MER)
B: Pyrimidinylpeptide
C: Pyrimidinylpeptide


Theoretical massNumber of molelcules
Total (without water)9,9563
Polymers9,9563
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)10 / 200Top-ranked ensemble
RepresentativeModel #1top-ranked ensemble

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Components

#1: RNA chain RNA (28-MER)


Mass: 8940.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UUCG-TAR RNA / Source: (gene. exp.) Human immunodeficiency virus 2 / Plasmid: puc19 / Production host: Escherichia coli (E. coli)
#2: Polypeptide(D) Pyrimidinylpeptide


Mass: 507.613 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: High resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H TOCSY
1432D 1H-1H NOESY
1542D 1H-1H NOESY
1623D (H)CCH-TOCSY
1723D (H)CCH-COSY
2813D 1H-15N NOESY
1923D 1H-13C NOESY
11022D H(C)N
11122D 1H-15N HSQC (2J)
11222D 1H-13C HSQC
21312D HNN-COSY
11422D H5NN-COSY
11523D forward-directed HCC-TOCSY-CCH E.COSY
21612D 1H-15N CPMG-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-1, 5.2 mM Pyrimidinylpeptide-2, 50 mM potassium chloride-3, 25 mM potassium phosphate-4, 90% H2O/10% D2O90% H2O/10% D2O
20.65 mM [U-100% 13C; U-100% 15N] UUCG-TAR-5, 5.2 mM Pyrimidinylpeptide-6, 50 mM potassium chloride-7, 25 mM potassium phosphate-8, 100% D2O100% D2O
30.65 mM UUCG-TAR-9, 5.2 mM Pyrimidinylpeptide-10, 50 mM potassium chloride-11, 25 mM potassium phosphate-12, 90% H2O / 10% D2O90% H2O/10% D2O
40.65 mM UUCG-TAR-13, 5.2 mM Pyrimidinylpeptide-14, 50 mM potassium chloride-15, 25 mM potassium phosphate-16, 100% D2O100% D2O
50.2 mM [U-100% 13C; U-100% 15N] UUCG-TAR-17, 0.8 mM Pyrimidinylpeptide-18, 50 mM potassium chloride-19, 25 mM potassium phosphate-20, 16 mg/mL Pf1 phage-21, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMUUCG-TAR-1[U-100% 13C; U-100% 15N]1
5.2 mMPyrimidinylpeptide-21
50 mMpotassium chloride-31
25 mMpotassium phosphate-41
0.65 mMUUCG-TAR-5[U-100% 13C; U-100% 15N]2
5.2 mMPyrimidinylpeptide-62
50 mMpotassium chloride-72
25 mMpotassium phosphate-82
0.65 mMUUCG-TAR-93
5.2 mMPyrimidinylpeptide-103
50 mMpotassium chloride-113
25 mMpotassium phosphate-123
0.65 mMUUCG-TAR-134
5.2 mMPyrimidinylpeptide-144
50 mMpotassium chloride-154
25 mMpotassium phosphate-164
0.2 mMUUCG-TAR-17[U-100% 13C; U-100% 15N]5
0.8 mMPyrimidinylpeptide-185
50 mMpotassium chloride-195
25 mMpotassium phosphate-205
16 mg/mLPf1 phage-215
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
175 6.2 ambient 298 K
275 6.2 ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker DRXBrukerDRX6005
Bruker AvanceBrukerAVANCE4006

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospindata analysis
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
HADDOCK2.1Dominguez, Boelens and Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 22 / NA beta-angle constraints total count: 4 / NA chi-angle constraints total count: 27 / NA epsilon-angle constraints total count: 5 / NA other-angle constraints total count: 22 / NA sugar pucker constraints total count: 95 / NOE constraints total: 567 / Hydrogen bond constraints total count: 60
NMR representativeSelection criteria: top-ranked ensemble
NMR ensembleConformer selection criteria: Top-ranked ensemble / Conformers calculated total number: 200 / Conformers submitted total number: 10

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