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Yorodumi- PDB-5i2v: NMR structure of a new G-quadruplex forming sequence within the K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i2v | ||||||||||||||||||||||||||||||||||
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Title | NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region | ||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / KRAS / proto-oncogene / cancer target | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / simulated annealing | Authors | Salgado, G.F. / Kerkour, A. / Mergny, J.-L. | Funding support | France, 3items |
Citation | Journal: J. Biol. Chem. / Year: 2017 | Title: High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation. Authors: Kerkour, A. / Marquevielle, J. / Ivashchenko, S. / Yatsunyk, L.A. / Mergny, J.L. / Salgado, G.F. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i2v.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i2v.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 5i2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i2v_validation.pdf.gz | 388.1 KB | Display | wwPDB validaton report |
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Full document | 5i2v_full_validation.pdf.gz | 537.3 KB | Display | |
Data in XML | 5i2v_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 5i2v_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i2v ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i2v | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 6986.514 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DNA G-quadruplex from the nuclease hypersensitive element of KRAS promotor region Source: (synth.) Homo sapiens (human) |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N, 90% H2O/10% D2O Label: no / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Details: 20 mM potassium phosphate pH ~6.6 with 70 mM KCl / Ionic strength: 90 mM / Ionic strength err: 2 / Label: Phosphate buffer / pH: 6.6 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 7 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 11 |