BMRB Entry 25049

Name: A Structure based mechanism for tRNA and retroviral RNA remodeling during primer annealing
Published: 2014-09-08

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PDB ID: 2mqt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25049
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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:

A Structure based mechanism for tRNA and retroviral RNA remodeling during primer annealing

Deposition date:

2015-10-16

Original release date:

2014-09-08

Authors:

D'Souza, Victoria; Yildiz, Zehra

Citation:

Citation: Miller, Sarah; Yildiz, F.; Lo, Jennifer; Wang, Bo; D'Souza, Victoria. "A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing" Nature 515, 591-595 (2014).
PubMed: 25209668

Assembly members:

Assembly members:
RNA_(68-MER), polymer, 68 residues, 21894.025 Da.

Natural source:

Natural source: Common Name: Murine Leukemia Virus Taxonomy ID: 11786 Superkingdom: Viruses Kingdom: not available Genus/species: Gammaretrovirus not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: in vitro transcription Vector: pNCA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(68-MER): GGGCGAGGGUCUCCUCUGAG UGAUUGACUACCCGUCAGCG GGGGUCUUUCAUUUGGGGGC UCGUGCCC

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	296
15N chemical shifts	27
1H chemical shifts	397

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (68-MER)	1

Entities:

Entity 1, RNA (68-MER) 68 residues - 21894.025 Da.

1

G

C

G

A

G

U

2

C

U

C

U

C

U

G

A

G

3

U

G

A

U

G

A

C

U

A

4

C

G

U

C

A

G

C

G

5

G

U

C

U

C

6

A

U

G

C

7

U

C

G

U

G

C

Samples:

sample_1: U5-PBS, [U-100% 13C; U-100% 15N], 0.8 mM; Tris 10 mM; NaCl 10 mM; D2O 100%

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; pressure: 1 atm; temperature: 311 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESYin H2O	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESYin D2O	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax, Guntert, Mumenthaler and Wuthrich, Johnson, One Moon Scientific - data analysis, processing, structure solution

NMR spectrometers:

Bruker DMX 700 MHz