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- PDB-2l5k: Solution structure of truncated 23-mer DNA MUC1 aptamer -

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Basic information

Entry
Database: PDB / ID: 2l5k
TitleSolution structure of truncated 23-mer DNA MUC1 aptamer
ComponentsDNA (5'-R(*(N68)P*G)-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*GP*GP*T)-3')
KeywordsDNA / NMR solution structure / DYANA and BCE models / TTT triloop containing DNA / truncated DNA MUC1 aptamer sequence / binding nucleotides
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, bioplymer chain elasticity
Model detailsfewest violations, model 1
AuthorsCognet, J. / Baouendi, M. / Hantz, E. / Missailidis, S. / Herve du Penhoat, C. / Piotto, M.
CitationJournal: Febs J. / Year: 2012
Title: Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR.
Authors: Baouendi, M. / Cognet, J.A. / Ferreira, C.S. / Missailidis, S. / Coutant, J. / Piotto, M. / Hantz, E. / Herve du Penhoat, C.
History
DepositionNov 2, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-R(*(N68)P*G)-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)8,1641
Polymers8,1641
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA (5'-R(*(N68)P*G)-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*GP*GP*T)-3')


Mass: 8164.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This entry contains the NMR solution structures (DYANA models 1-20)and a Biopolymer Chain Elasticity structure (BCE model 21) of the truncated 23-mer DNA MUC1 aptamer. The coordinates of two ...Details: This entry contains the NMR solution structures (DYANA models 1-20)and a Biopolymer Chain Elasticity structure (BCE model 21) of the truncated 23-mer DNA MUC1 aptamer. The coordinates of two bridging water molcules are available for model 21 upon request to J. Cognet. The 23-mer sequence was extracted from the S1.3/S2.2 total MUC1 aptamer sequence reported previously (Ferreira et al, Tumor Biology 2006). The 23-mer sequence includes all of the nucleotides that bind the VNTR MUC1 peptides. NMR data were obtained for a longer sequence (25-mer with dangling ends on both 5' and 3' ends) but the sequence was shortened to facilitate convergence in the simulated annealing (DYANA) protocol. VNTR peptides are targets for tumour diagnostics and therapeutics.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H TOCSY
1222D 1H-13C HSQC
1322D 1H-31P COSY
1422D DQF-COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1712D 1H-1H TOCSY
1812D 1H-1H NOESY
2932D 1H-1H TOCSY
21032D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 5 uM sodium azide, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
22 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide, 100% D2O100% D2O
31 mM DNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 5 uM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3')-11
20 mMsodium phosphate-21
5 uMsodium azide-31
50 mMsodium chloride-41
2 mMDNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3')-52
20 mMsodium phosphate-62
50 mMsodium chloride-72
5 uMsodium azide-82
1 mMDNA (5'-D(*CP*AP*GP*TP*TP*GP*AP*TP*CP*CP*TP*TP*TP*GP*GP*AP*TP*AP*CP*CP*CP*TP*G)-3')-93
20 mMsodium phosphate-103
50 mMsodium chloride-113
5 uMsodium azide-123
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1506.5ambient 298 K
2506.51 atm264.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS5001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun and Wuthrichrefinement
PROSA6.0.2Guntertprocessing
XEASY1.2Bartels et al.chemical shift assignment
XEASY1.2Bartels et al.peak picking
NMRPipe1998Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
Smol1(SMOL) Pakleza, Santini, Cognetstructure solution
RefinementMethod: simulated annealing, bioplymer chain elasticity / Software ordinal: 1
Details: 100 structures were calculated with DYANA and the 20 structures with the smallest residual target function have been refined by energy minimization with AMBER before being deposited., A ...Details: 100 structures were calculated with DYANA and the 20 structures with the smallest residual target function have been refined by energy minimization with AMBER before being deposited., A model with the NMR-defined torsion angles was constructed with the BCE method and AMBER energy refined. It contains 2 bridging water molecules (coordinates available upon request to J. Cognet).
NMR constraintsNA alpha-angle constraints total count: 24 / NA beta-angle constraints total count: 23 / NA chi-angle constraints total count: 23 / NA delta-angle constraints total count: 23 / NA epsilon-angle constraints total count: 22 / NA gamma-angle constraints total count: 22 / NA other-angle constraints total count: 24 / NA sugar pucker constraints total count: 55 / NOE constraints total: 607 / NOE intraresidue total count: 198 / NOE long range total count: 35 / NOE medium range total count: 4 / NOE sequential total count: 161
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 0.2 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 0.04 ° / Maximum upper distance constraint violation: 0.14 Å
Torsion angle constraint violation method: potential energy function
NMR ensemble rmsDistance rms dev: 0.61 Å / Distance rms dev error: 0.02 Å

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