BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 19728

Title: A tetrahelical DNA fold adopted by alternating GGG and GCG tracts   PubMed: 25500730

Deposition date: 2014-01-10 Original release date: 2014-12-22

Authors: Kocman, Vojc; Plavec, Janez

Citation: Kocman, Vojc; Plavec, Janez. "A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts"  Nat. Commun. 5, 5831-5831 (2014).

Assembly members:
d(GGGAGCG)n, polymer, 15 residues, 4765.122 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):
d(GGGAGCG)n: GGGAGCGAGGGAGCG

Data sets:
Data typeCount
1H chemical shifts112

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_11
2DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_21

Entities:

Entity 1, DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3')_1 15 residues - 4765.122 Da.

1   DGDGDGDADGDCDGDADGDG
2   DGDADGDCDG

Samples:

VK1: DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3') 2.8 mM; DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3'), partial residue specific 15N, 1 mM; DNA (5'-D(*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*G)-3'), residue specific 2H, 1 mM; H2O 90%; D2O 10%; LiCl 100 mM

VK1_sample_conditions: ionic strength: 100 mM; pH: 6; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYVK1isotropicVK1_sample_conditions
2D DQF-COSYVK1isotropicVK1_sample_conditions
2D 1H-1H TOCSYVK1isotropicVK1_sample_conditions
2D 1H-31P COSYVK1isotropicVK1_sample_conditions
2D 1H-15N HSQCVK1isotropicVK1_sample_conditions

Software:

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

  • Agilent VNMRS 800 MHz
  • Agilent VNMRS 600 MHz
  • Agilent DD2 600 MHz