BMRB Entry 18239

Name: Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus
Published: 2012-03-12

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PDB ID: 2lp9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18239
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:

Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus

Deposition date:

2012-02-06

Original release date:

2012-03-12

Authors:

Skov, Joan

Citation:

Citation: Skov, Joan; Gaudin, Mathieu; Podbevsek, Peter; Olsthoorn, Rene; Petersen, Michael. "The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter." RNA 18, 992-1000 (2012).
PubMed: 22393035

Assembly members:

Assembly members:
RNA_(5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3')_, polymer, 16 residues, 5122.140 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*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3')_: GAGGACAUAGAUCUUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	105
31P chemical shifts	15

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPAPGPGPAPCPAPUPAPGPAPUPCPUPUPC)-3')	1

Entities:

Entity 1, RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*AP*UP*CP*UP*UP*C)-3') 16 residues - 5122.140 Da.

1

G

A

G

A

C

A

U

A

G

2

A

U

C

U

C

Samples:

sample_1: wt_RNA 2 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 65 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR v3.851, Brunger - structure solution

NMR spectrometers:

Varian INOVA 500 MHz