+Open data
-Basic information
Entry | Database: PDB / ID: 2l5k | ||||||||||||||||||||
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Title | Solution structure of truncated 23-mer DNA MUC1 aptamer | ||||||||||||||||||||
Components | DNA (5'-R(*Keywords | DNA / NMR solution structure / DYANA and BCE models / TTT triloop containing DNA / truncated DNA MUC1 aptamer sequence / binding nucleotides | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, bioplymer chain elasticity | Model details | fewest violations, model 1 | Authors | Cognet, J. / Baouendi, M. / Hantz, E. / Missailidis, S. / Herve du Penhoat, C. / Piotto, M. | Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l5k.cif.gz | 286.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l5k.ent.gz | 237.4 KB | Display | PDB format |
PDBx/mmJSON format | 2l5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l5k_validation.pdf.gz | 300 KB | Display | wwPDB validaton report |
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Full document | 2l5k_full_validation.pdf.gz | 373.7 KB | Display | |
Data in XML | 2l5k_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 2l5k_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/2l5k ftp://data.pdbj.org/pub/pdb/validation_reports/l5/2l5k | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 8164.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
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-Experimental details
-Experiment
Experiment | Method: 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. | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 constraints | NA 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 representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||
NMR ensemble | Average 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 rms | Distance rms dev: 0.61 Å / Distance rms dev error: 0.02 Å |