BMRB Entry 30184

Name: Solution structure of parallel stranded adenosine duplex r(AAAA)-dA-r(AAA)
Published: 2017-08-04

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PDB ID: 5tgg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30184
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of parallel stranded adenosine duplex r(AAAA)-dA-r(AAA)

Deposition date:

2016-09-27

Original release date:

2017-08-04

Authors:

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

Citation:

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).
PubMed: 28973475

Assembly members:

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:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	95

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1

Entities:

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

1

DT

A2M

DA

A2M

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 31P-1H HSQC	sample_2	isotropic	sample_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