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- PDB-1qc8: NMR STRUCTURE OF TAU EXON 10 SPLICING REGULATORY ELEMENT RNA -

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Basic information

Entry
Database: PDB / ID: 1qc8
TitleNMR STRUCTURE OF TAU EXON 10 SPLICING REGULATORY ELEMENT RNA
ComponentsTAU EXON 10 SPLICING REGULATORY ELEMENT RNA
KeywordsRNA / ALTERNATIVE MRNA SPLICING / FRONTOTEMPORAL DEMENTIA FTDP-17 / INTRONIC MUTATIONS / STEM-LOOP RNA STRUCTURE / TAU GENE EXON 10
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / COMPLETELY RANDOM STARTING COORDINATES X-PLOR BASED SIMULATED ANNEALING PROTOCOL
AuthorsVarani, L. / Spillantini, M.G. / Klug, A. / Goedert, M. / Varani, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17.
Authors: Varani, L. / Hasegawa, M. / Spillantini, M.G. / Smith, M.J. / Murrell, J.R. / Ghetti, B. / Klug, A. / Goedert, M. / Varani, G.
History
DepositionMay 18, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAU EXON 10 SPLICING REGULATORY ELEMENT RNA


Theoretical massNumber of molelcules
Total (without water)7,9911
Polymers7,9911
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)29 / 50structures with the lowest energy
Representative

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Components

#1: RNA chain TAU EXON 10 SPLICING REGULATORY ELEMENT RNA


Mass: 7990.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 13C-SEPARATED NOESY
131DQF-COSY
1412D TOCSY

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Sample preparation

Details
Solution-IDContents
11MM RNA, 10MM NAPHOSPHATE BUFFER PH 6
21MM RNA, U 15N,13C, 10MM NAPHOSPHATE BUFFER PH 6
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
110mM NAPHOSPHATE BUFFER PH 6 6300 K
210mM NAPHOSPHATE BUFFER PH 6 6300 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
UXNMRcollection
Felix2.1processing
Felix97data analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: COMPLETELY RANDOM STARTING COORDINATES X-PLOR BASED SIMULATED ANNEALING PROTOCOL
Software ordinal: 1
Details: NOE DISTANCE CONSTRAINTS: 564, INTRARESIDUE: 331, SEQUENTIAL: 181, LONG AND MEDIUM RANGE: 52, HYDROGEN BONDING AND PLANARITY CONSTRAINTS: 90, DIHEDRAL CONSTRAINTS: 124, TOTAL EXPERIMENTAL ...Details: NOE DISTANCE CONSTRAINTS: 564, INTRARESIDUE: 331, SEQUENTIAL: 181, LONG AND MEDIUM RANGE: 52, HYDROGEN BONDING AND PLANARITY CONSTRAINTS: 90, DIHEDRAL CONSTRAINTS: 124, TOTAL EXPERIMENTAL CONSTRAINTS: 778, AVERAGE NUMBER PER NUCLEOTIDE: 31.1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 29

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