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- PDB-1jtw: Structure of SL4 RNA from the HIV-1 Packaging Signal -

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Entry
Database: PDB / ID: 1jtw
TitleStructure of SL4 RNA from the HIV-1 Packaging Signal
Components5'-R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3'
KeywordsRNA / hairpin / tandem G-U pairs / GAGA tetraloops
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsKerwood, D.J. / Cavaluzzi, M.J. / Borer, P.N.
CitationJournal: Biochemistry / Year: 2001
Title: Structure of SL4 RNA from the HIV-1 packaging signal.
Authors: Kerwood, D.J. / Cavaluzzi, M.J. / Borer, P.N.
History
DepositionAug 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 23, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,57716
Polymers5,2321
Non-polymers34515
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 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 5232.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs in the packaging signal of HIV-1.
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Sodium ions which were distant from the RNA were removed.

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Sample preparation

DetailsContents: ~0.7mM SL4 concentration in buffer: 25mM NaCl, 5mM NaHPO4 (pH 7.0), 0.1mM EDTA, 0.01% NaN3
Solvent system: 99.96% D2O or 90% H2O, 10% D2O
Sample conditionspH: 7.0 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Wuthrichrefinement
Amber5Kollmanstructure solution
RefinementSoftware ordinal: 1
Details: DYANA structures were further refined with the molecular dynamics and minimization program, AMBER.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 14

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