BMRB Entry 34054
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34054
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Title: Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene PubMed: 28513602
Deposition date: 2016-10-13 Original release date: 2017-05-25
Authors: Kocman, V.; Plavec, J.
Citation: Kocman, V.; Plavec, J.. "Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions." Nat. Commun. 8, 15355-15355 (2017).
Assembly members:
entity_1, polymer, 15 residues, 4765.084 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: GCGAGGGAGCGAGGG
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 103 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
| 3 | entity_1, 3 | 1 |
| 4 | entity_1, 4 | 1 |
Entities:
Entity 1, entity_1, 1 15 residues - 4765.084 Da.
| 1 | DG | DC | DG | DA | DG | DG | DG | DA | DG | DC | ||||
| 2 | DG | DA | DG | DG | DG |
Samples:
sample_1: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') 1.0 mM; sodium chloride 150 mM
sample_2: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), residue specific 15N and 13C, 1 mM; sodium chloride 150 mM
sample_3: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), D8 residue specific labeled, 1 mM; sodium chloride 150 mM
sample_4: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), uniformly labeled with D8, 1 mM; sodium chloride 150 mM
sample_conditions_1: ionic strength: 150 mM; pH: 6; pressure: 1 atm; temperature: 273 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 1D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_4 | isotropic | sample_conditions_1 |
Software:
AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation
SPARKY, Goddard - chemical shift assignment
spar - peak picking
NMR spectrometers:
- Agilent-Varian Uniform NMR System 600 MHz
- Agilent-Varian Uniform NMR System 800 MHz