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- PDB-2kdq: Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequence... -

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Basic information

Entry
Database: PDB / ID: 2kdq
TitleSimultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein
Components
  • HIV-1 TAR RNA
  • L-22 CYCLIC PEPTIDE
KeywordsRNA binding protein/RNA / PEPTIDOMIMETICS / PEPTIDE STRUCTURE / RNA RECOGNITION / IMMUNODEFICIENCY VIRUS / TAR RNA / mimic of RNA binding protein / RNA binding protein-RNA COMPLEX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 7
AuthorsDavidson, A. / Leeper, T.C. / Varani, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein
Authors: Davidson, A. / Leeper, T.C. / Athanassiou, Z. / Patora-Komisarska, K. / Karn, J. / Robinson, J.A. / Varani, G.
History
DepositionJan 14, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 23, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-22 CYCLIC PEPTIDE
B: HIV-1 TAR RNA


Theoretical massNumber of molelcules
Total (without water)11,0762
Polymers11,0762
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)10 / 100Lowest energy, least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide L-22 CYCLIC PEPTIDE


Mass: 1768.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE L-22 PEPTIDE WAS SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC
#2: RNA chain HIV-1 TAR RNA


Mass: 9307.555 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS TRANSCRIBED IN VITRO FROM DNA OLIGONUCLEOTIDE TEMPLATES WITH T7 RNA POLYMERASE PURIFIED IN HOUSE WITH UNLABELED OR 13C/15N ENRICHED NTPS (ISOTEC) AND PURIFIED BY DENATURING PAGE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D-13C HMQC NOESY, 3D (H)CCH TOCSY, IPAP-HSQC
22415N HSQC
1312D NOESY
2422D WATERGATE NOESY
153F1fF2f-type NOESY, F1fF2f-type TOCSY, 2D (H)CCH-COSY
1652D 1H-1H NOESY
274F1fF2f-type WATERGATE NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM HIV-1 TAR RNA-1, 1.0mM L-22 CYCLIC PEPTIDE-2, 100% D2O100% D2O
21.0mM HIV-1 TAR RNA-3, 1.0mM L-22 CYCLIC PEPTIDE-4, 90 % H2O, 10% D2O90% H2O/10% D2O
31.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-5, 1.0mM L-22 CYCLIC PEPTIDE-6, 100% D2O100% D2O
41.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-7, 1.0mM L-22 CYCLIC PEPTIDE-8, 90 % H2O, 10% D2O90% H2O/10% D2O
51.0mM [U-2H] HIV-1 TAR RNA-9, 1.0mM L-22 CYCLIC PEPTIDE-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity_3-11
1.0 mMentity_6-21
1.0 mMentity_3-32
1.0 mMentity_6-42
1.0 mMentity_3-5[U-98% 13C; U-98% 15N]3
1.0 mMentity_6-63
1.0 mMentity_3-7[U-98% 13C; U-98% 15N]4
1.0 mMentity_6-84
1.0 mMentity_3-9[U-2H]5
1.0 mMentity_6-105
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM potassium phosphate 6.6 ambient 298 K
210 mM potassium phosphate 6.6 ambient 277 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX6002
Varian InovaVarianINOVA8003
Bruker AVIIIBrukerAVIII6004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16.0C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
X-PLOR NIH2.16.0C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures of the HIV-1 TAR RNA/L-22 complex were calculated with Xplor-NIH. Backbone dihedral angle restraints for the peptide were estimated using chemical shift data and TALOS. Structures ...Details: Structures of the HIV-1 TAR RNA/L-22 complex were calculated with Xplor-NIH. Backbone dihedral angle restraints for the peptide were estimated using chemical shift data and TALOS. Structures were originally calculated without RDCs to test for convergence and adherence to the NOE data. RDC restraints were then applied as susceptibility anisotropy restraints with a harmonic potential well.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest energy, least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 7

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