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- PDB-2juk: guanidino neomycin B recognition of an HIV-1 RNA helix -

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Basic information

Entry
Database: PDB / ID: 2juk
Titleguanidino neomycin B recognition of an HIV-1 RNA helix
ComponentsHIV-1 frameshift site RNA
KeywordsRNA / HIV-1 / RNA-ligand interactions / guanidinoglycosides
Function / homologyChem-G0B / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsStaple, D.W. / Venditti, V. / Niccolai, N. / Elson-Schwab, L. / Tor, Y. / Butcher, S.E.
CitationJournal: Chembiochem / Year: 2008
Title: Guanidinoneomycin B Recognition of an HIV-1 RNA Helix.
Authors: Staple, D.W. / Venditti, V. / Niccolai, N. / Elson-Schwab, L. / Tor, Y. / Butcher, S.E.
History
DepositionAug 30, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 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: HIV-1 frameshift site RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9442
Polymers7,0711
Non-polymers8731
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain HIV-1 frameshift site RNA


Mass: 7071.299 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-G0B / (1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside


Mass: 872.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H64N18O13

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D HMBC
1412D 1H-13C HSQC
1512D 1H-13C HSQC

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Sample preparation

DetailsContents: 1mM mM HIV-1 frameshift site RNA, 0.5mM mM [U,G,C,A] 100% 15N, 100% 13C HIV-1 frameshift site RNA, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHIV-1 frameshift site RNA1
0.5 mMHIV-1 frameshift site RNA[U,G,C,A] 100% 15N, 100% 13C2
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Varian INOVAVarianINOVA9003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameDeveloperClassification
AmberCase, D.A. et al.refinement
CNSBrunger, A.T. et al.structure solution
MOLMOLKoradi, R. et al.structure visualization
SparkyGoddard, T.D. et al.chemical shift assignment
X-PLOR NIHSchwieters, C.D. et al.structure solution
XwinNMRBruker Biospincollection
NMRPipeDelaglio, F. et al.collection
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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