BMRB Entry 17601

Name: Solution structure of the MLV readthrough pseudoknot
Published: 2011-12-02

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PDB ID: 2lc8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17601
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the MLV readthrough pseudoknot

Deposition date:

2011-04-26

Original release date:

2011-12-02

Authors:

Houck-Loomis, Brian; Durney, Michael; D'Souza, Victoria

Citation:

Citation: Houck-Loomis, Brian; Durney, Michael; Salguero, Carolina; Shankar, Neelaabh; Nagle, Julia; Goff, Stephen. "An equilibrium-dependent retroviral mRNA switch regulates translational recoding." Nature 480, 561-564 (2011).
PubMed: 22121021

Assembly members:

Assembly members:
RNA_(59-MER), polymer, 63 residues, 111.103 Da.

Natural source:

Natural source: Common Name: MMLV Taxonomy ID: 11801 Superkingdom: Viruses Kingdom: not available Genus/species: not available murine leukemia virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: None: in vitro transcription Vector: pUC19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(59-MER): GGAGGUCAGGGUCAGGAGCC CCCCCCUGAACCCAGGAUAA CCCUCAAAGUCGGGGGGCAA CCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	92
1H chemical shifts	182

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA_(59-MER)	1

Entities:

Entity 1, RNA_(59-MER) 63 residues - 111.103 Da.

1

G

A

G

U

C

A

G

2

G

U

C

A

G

A

G

C

3

C

U

G

A

4

C

A

G

A

U

A

5

C

U

C

A

G

U

6

C

G

C

A

7

C

Samples:

MLV-PK: RNA (59-MER)0.2 – 2.0 mM; D2O 100%

MLV-PK-AC-13C_15N: RNA (59-MER), [U-100% 13C; U-100% 15N], 0.2 – 2.0 mM; D2O 100%

MLV-PK-AC-2H: RNA (59-MER), [U-100% 2H], 0.2 – 2.0 mM; D2O 100%

sample_conditions_1: ionic strength: 0.02 M; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	MLV-PK	isotropic	sample_conditions_1
2D 1H-13C HSQC	MLV-PK-AC-13C_15N	isotropic	sample_conditions_1
2D 1H-13C HSQC	MLV-PK-AC-13C_15N	isotropic	sample_conditions_1
2D 1H-1H NOESY	MLV-PK-AC-2H	isotropic	sample_conditions_1
2D 1H-1H NOESY	MLV-PK-AC-13C_15N	isotropic	sample_conditions_1
2D 1H-1H NOESY	MLV-PK	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 900 MHz