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- PDB-1e95: Solution structure of the pseudoknot of SRV-1 RNA, involved in ri... -

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Basic information

Entry
Database: PDB / ID: 1.0E+95
TitleSolution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting
ComponentsRNA (5'-(*GP*CP*GP*GP*CP*CP*AP*GP*CP*UP*CP* CP*AP*GP*GP*CP*CP*GP*CP*CP*AP*AP*AP*CP* AP*AP*UP*AP*UP*GP*GP*AP*GP*CP*AP*C)-3')
KeywordsRNA / RIBONUCLEIC ACID / SRV-1 / PSEUDOKNOT / FRAMESHIFT
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesSIMIAN RETROVIRUS 1
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMichiels, P.J.A. / Versleyen, A. / Pleij, C.W.A. / Hilbers, C.W. / Heus, H.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution Structure of the Pseudoknot of Srv-1 RNA, Involved in Ribosomal Frameshifting
Authors: Michiels, P.J.A. / Versleijen, A.A. / Verlaan, P.W. / Pleij, C.W.A. / Hilbers, C.W. / Heus, H.A.
History
DepositionOct 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,5851
Polymers11,5851
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)15 / 100LEAST RESTRAINT VIOLATIONS, LOWEST ENERGY
Representative

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Components

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


Mass: 11585.017 Da / Num. of mol.: 1 / Fragment: GAG-PRO FRAMESHIFTING PSEUDOKNOT / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SIMIAN RETROVIRUS 1 / References: EMBL: M11841
Compound detailsCHAIN A ENGINEERED MUTATION G2C, C10U, C18G, G35A, DELTA(G26, C27, U28)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
14131P-1H HETCOR
151HMQC
16131P-1H HETERO-TOCSY-NOESY
171NOESY-HMQC
181(H)CCH-TOCSY

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Sample preparation

Sample conditionsIonic strength: 100 MM NACL, 10 MM K2HPO4/KH2PO4 / pH: 6.4 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS, LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 15

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