BMRB Entry 16951

Name: The Structure of RNA Internal Loops with Tandem AG Pairs: 5&#039;GAGC/3&#039;CGAG
Published: 2010-07-02

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PDB ID: 2ky0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16951
MolProbity Validation Chart

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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:

The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG

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).
PubMed: 20481618

Assembly members:

Assembly members:
RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*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:

Experimental source: Production method: obtained from a vendor

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	50
1H chemical shifts	107
31P chemical shifts	10

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPAPCPGPAPGPCPGPUPCP*A)-3')_1	1
2	RNA (5'-R(GPAPCPGPAPGPCPGPUPCP*A)-3')_2	1

Entities:

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

1

G

A

C

G

A

G

C

G

U

C

2

A

Samples:

sample_1: RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*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*GP*AP*GP*CP*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: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-31P HETCOR	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_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