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- PDB-1ei2: STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE T... -

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Basic information

Entry
Database: PDB / ID: 1ei2
TitleSTRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE TAU EXON 10 SPLICING REGULATORY ELEMENT BY AMINOGLYCOSIDE ANTIBIOTICS
ComponentsTAU EXON 10 SRE RNA
KeywordsRNA / tau / frontotemporal dementia FTDP-17 / intronic mutations / aminoglycoside / RNA major groove recognition
Function / homologyNEOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsVarani, L. / Spillantini, M.G. / Goedert, M. / Varani, G.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Structural basis for recognition of the RNA major groove in the tau exon 10 splicing regulatory element by aminoglycoside antibiotics.
Authors: Varani, L. / Spillantini, M.G. / Goedert, M. / Varani, G.
History
DepositionFeb 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAU EXON 10 SRE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6052
Polymers7,9911
Non-polymers6151
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 50structures with the least restraint violations, structures with the lowest energy
Representative

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Components

#1: RNA chain TAU EXON 10 SRE RNA


Mass: 7990.780 Da / Num. of mol.: 1 / Fragment: TAU EXON 10 SPLICING REGULATORY ELEMENT / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1312D TOCSY
1412D 13C HSQC
1512D 15N HSQC
161HCCP, HETEROTOCSY

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Sample preparation

DetailsContents: 1mM tau exon 10 SRE RNA U-13C,15N; 10mM phosphate buffer, pH 6; 1mM neomycin unlabelled
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM potassium phosphate / pH: 6 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8Brungerstructure solution
Felix97msidata analysis
XwinNMR2brukercollection
X-PLOR3.8Brungerrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
Details: The structure was calculated starting from random coordinates. No manual or automatic docking step was used at any stage of the calculation.
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 17

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