BMRB Entry 17406

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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/BMR17406
MolProbity Validation Chart

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Title:
Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon
Deposition date:
2011-01-11
Original release date:
2011-08-17
Authors:
Lerman, Yelena; Kennedy, Scott; Turner, Douglas
Citation:

Citation: Lerman, Yelena; Kennedy, Scott; Shankar, Neelaabh; Parisien, Marc; Major, Francois; Turner, Douglas. "NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions."  RNA 17, 1664-1677 (2011).
PubMed: 21778280

Assembly members:

Assembly members:
RNA_(5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), polymer, 11 residues, 3522.178 Da.
RNA_(5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), polymer, 11 residues, 3545.218 Da.

Natural source:

Natural source:   Common Name: silkworm   Taxonomy ID: 7091   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Bombyx mori

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'): GUGAAGCCCGU
RNA_(5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'): CGGAGGACACU

Data sets:
Data typeCount
13C chemical shifts24
15N chemical shifts8
1H chemical shifts156
31P chemical shifts20

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')1
2RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')2

Entities:

Entity 1, RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3') 11 residues - 3522.178 Da.

1   GUGAAGCCCG
2   U

Entity 2, RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3') 11 residues - 3545.218 Da.

1   CGGAGGACAC
2   U

Samples:

sample_1: RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3') 1.5 mM; RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3') 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_2: RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3') 1.5 mM; RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3') 1.5 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 0.1 M; pH: 5; pressure: 1 atm; temperature: 273 K

sample_conditions_3: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_3
2D 1H-1H NOESYsample_2isotropicsample_conditions_3
2D 1H-1H TOCSYsample_2isotropicsample_conditions_3
2D 1H-1H TOCSYsample_2isotropicsample_conditions_3
2D 1H-1H COSYsample_2isotropicsample_conditions_3
2D 31P-1H COSYsample_2isotropicsample_conditions_3

Software:

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.114, Goddard - chemical shift assignment, data analysis

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

VNMR v6.1C, Varian - collection

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

NMR spectrometers:

  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz