BMRB Entry 16950

Title:
The Structure of RNA Internal Loops with Tandem AG Pairs: 5'AAGU/3'UGAA   PubMed: 20481618
Deposition date:
2010-05-25
Original release date:
2010-07-02
Authors:
Hammond, Nicholas; Kennedy, Scott; Turner, Douglas
Citation:

Citation: Hammond, Nicholas; Tolbert, Blanton; Kierzek, Ryszard; Turner, Douglas; Kennedy, Scott. "RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA."  Biochemistry 49, 5817-5827 (2010).

Assembly members:

Assembly members:
RNA_(5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3'), polymer, 11 residues, 3530.203 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: obtained from a vendor

Experimental source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3'): GACAAGUGUCA

Data sets:
Data typeCount
13C chemical shifts29
15N chemical shifts4
1H chemical shifts104
31P chemical shifts10

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')_11
2RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')_21

Entities:

Entity 1, RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3')_1 11 residues - 3530.203 Da.

1   GACAAGUGUC
2   A

Samples:

sample_1: RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3') 1 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; H2O 90%; D2O 10%

sample_2: RNA (5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3') 1 mM; sodium chloride 80 mM; sodium phosphate 10 mM; EDTA 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 0.1 M; pH: 6.1; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-31P HETCORsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2

Software:

SPARKY v3.12, Goddard - chemical shift assignment, data analysis

VNMR v6.1C, Varian - collection

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

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz