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 30184

Title: Solution structure of parallel stranded adenosine duplex r(AAAA)-dA-r(AAA)   PubMed: 28973475

Deposition date: 2016-09-27 Original release date: 2017-08-04

Authors: Denisov, A.; Noronha, A.; Gehring, K.; Wilds, C.

Citation: Copp, William; Denisov, Alexey; Xie, Jingwei; Noronha, Anne; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher; Gehring, Kalle. "Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA."  Nucleic Acids Res. 45, 10321-10331 (2017).

Assembly members:
RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3'), polymer, 9 residues, 2975.072 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):
RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3'): XXXXXXXXX

Data sets:
Data typeCount
1H chemical shifts95

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, chain 11
2entity_1, chain 21

Entities:

Entity 1, entity_1, chain 1 9 residues - 2975.072 Da.

1   DTA2MA2MA2MA2MDAA2MA2MA2M

Samples:

sample_1: TA8 duplex 1.0 mM; H2O 90%; D2O 10%

sample_2: TA8 duplex 1.0 mM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 4.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 50 mM; pH: 4.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 31P-1H HSQCsample_2isotropicsample_conditions_2

Software:

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - data analysis

VNMR, Varian - collection

NMR spectrometers:

  • Varian UNITY 800 MHz
  • Varian VNMRS 500 MHz