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- PDB-1kis: TAR-TAR "KISSING" HAIRPIN COMPLEX DERIVED FROM THE HIV GENOME, NM... -

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Basic information

Entry
Database: PDB / ID: 1kis
TitleTAR-TAR "KISSING" HAIRPIN COMPLEX DERIVED FROM THE HIV GENOME, NMR, 1 STRUCTURE
Components
  • RNA (5'-R(*GP*AP*GP*CP*CP*CP*UP*GP*GP*GP*AP*GP*GP*CP*UP*C)-3')
  • RNA (5'-R(*GP*CP*UP*GP*UP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3')
KeywordsRNA / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsChang, K.Y. / Tinoco Jr, I.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement.
Authors: Chang, K.Y. / Tinoco Jr., I.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Characterization of a "Kissing" Hairpin Complex Derived from the Human Immunodeficiency Virus Genome
Authors: Chang, K.Y. / Tinoco Jr, I.
History
DepositionJun 11, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 21, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _entity.details / _entity.pdbx_fragment / _ndb_struct_conf_na.feature / _pdbx_database_status.process_site / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_refine.details / _pdbx_nmr_refine.method / _pdbx_nmr_spectrometer.field_strength / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,2412
Polymers10,2412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area5990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 17structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5168.135 Da / Num. of mol.: 1 / Fragment: TRANSCRIPTIONAL ACTIVATION RESPONSE (TAR) REGION / Source method: obtained synthetically
Details: THE OLIGONUCLEOTIDES WERE SYNTHESIZED ENZYMATICALLY.
Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*GP*CP*UP*GP*UP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3')


Mass: 5073.071 Da / Num. of mol.: 1 / Fragment: COMPLEMENTARY LOOP SEQUENCE (TAR*) REGION / Source method: obtained synthetically
Details: THE OLIGONUCLEOTIDES WERE SYNTHESIZED ENZYMATICALLY.
Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: simulated annealing-restrained molecular dynamics protocol followed by an energy minimization step
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 17 / Conformers submitted total number: 1

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