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- PDB-1s9s: SOLUTION STRUCTURE OF MLV PSI SITE -

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Basic information

Entry
Database: PDB / ID: 1s9s
TitleSOLUTION STRUCTURE OF MLV PSI SITE
ComponentsMLV Psi encapsidation site
KeywordsRNA / MLV / A-MINOR K-TURN / STEM LOOP / BULGE / G-U MISMATCH / G-A MISMATCH / U-U MISMATCH / A-C MISMATCH
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsD'Souza, V. / Dey, A. / Habib, D. / Summers, M.F.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: NMR structure of the 101-nucleotide core encapsidation signal of the Moloney Murine Leukemia Virus.
Authors: D'Souza, V. / Dey, A. / Habib, D. / Summers, M.F.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MLV Psi encapsidation site


Theoretical massNumber of molelcules
Total (without water)32,7031
Polymers32,7031
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 / -
Representative

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Components

#1: RNA chain MLV Psi encapsidation site


Mass: 32703.430 Da / Num. of mol.: 1 / Fragment: Stem loop BCD / Source method: obtained synthetically
Details: THIS SEQUENCE WAS SYNTHESIZED BY IN VITRO TRANSCRIPTION USING A LINEARIZED DNA PLASMID AS TEMPLATE AND T7 RNA POLYMERASE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D ROESY
1312D HMQC
1413D 13C-separated NOESY
1514D 13C-separated NOESY
2622D WATERGATE NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Psi MONOMERIC RNA GUA-15N,13C, 10mM Tris, 100% D2O100% D2O
21.2 mM Psi MONOMERIC RNA ADE-15N,13C, 10mM Tris, 100% D2O100% D2O
31.2 mM Psi MONOMERIC RNA URA-15N,13C, 10mM Tris, 100% D2O100% D2O
41.2 mM Psi MONOMERIC RNA CYT-15N,13C, 10mM Tris, 100% D2O100% D2O
51.2 mM Psi MONOMERIC RNA GUA-URA-15N, 90% H2O, 10% D2O90% H2O/10% D2O
61.2 mM Psi MONOMERIC RNA GUA-URA-CYT-2H, 10mM Tris, 100% D2O100% D2O
71.2 mM Psi MONOMERIC RNA GUA-URA-ADE-2H, 10mM Tris, 100% D2O100% D2O
81.2 mM Psi MONOMERIC RNA GUA-CYT-ADE-2H, 10mM Tris, 100% D2O100% D2O
91.2 mM Psi MONOMERIC RNA ADE-URA-CYT-2H, 10mM Tris, 100% D2O100% D2O
100.6 mM SL-B MONOMERIC RNA 15N,13C, 10mM Tris, 0.1 mM EDTA, 100% D2O100% D2O
110.6 mM SL-C MONOMERIC RNA 15N,13C, 10mM Tris, 0.1 mM EDTA, 100% D2O100% D2O
120.6 mM SL-D MONOMERIC RNA 15N,13C, 10mM Tris, 0.1 mM EDTA, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM NaCl 7ambient 308 K
25 mM NaCl 7ambient 283 K
35 mM NaCl 7ambient 308 K
45 mM NaCl 7ambient 308 K
55 mM NaCl 7ambient 308 K
65 mM NaCl 7ambient 283 K
75 mM NaCl 7ambient 308 K
85 mM NaCl 7ambient 308 K
95 mM NaCl 7ambient 308 K
105 mM NaCl 7ambient 283 K
115 mM NaCl 7ambient 308 K
125 mM NaCl 7ambient 308 K

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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 AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
NMRView5.0.3Bruce A. Johnsondata analysis
CYANArefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR ensembleConformers submitted total number: 20

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