BMRB Entry 11607

Name: Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish
Published: 2017-02-06

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PDB ID: 2rvo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11607
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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:

Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish

Deposition date:

2016-02-03

Original release date:

2017-02-06

Authors:

Otsu, Maina; Norose, Nao; Arai, Nao; Terao, Ryo; Kajikawa, Masaki; Okada, Norihiro; Kawai, Gota

Citation:

Citation: Otsu, Maina; Norose, Nao; Arai, Nao; Terao, Ryo; Kajikawa, Masaki; Okada, Norihiro; Kawai, Gota. "Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish" .

Assembly members:

Assembly members:
RNA_(34-MER), polymer, 34 residues, 10859.578 Da.

Natural source:

Natural source: Common Name: zebrafish Taxonomy ID: 7955 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Denio Renio

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(34-MER): GGCGCUUUGACACAAUCUAC AUUGUAAAAGCGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	33
1H chemical shifts	97

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (34-MER)	1

Entities:

Entity 1, RNA (34-MER) 34 residues - 10859.578 Da.

1

G

C

G

C

U

G

A

2

C

A

C

A

U

C

U

A

C

3

A

U

G

U

A

G

4

C

G

C

Samples:

ZfL2-1-34_D2O: RNA (34-MER) 0.3 mM; RNA (34-MER), [U-100% 13C; U-100% 15N], 0.26 mM; sodium phosphate 20 mM; sodium chloride 50 mM; D2O, [U-2H], 100%

ZfL2-1-34_H2O: RNA (34-MER), [U-13C; U-15N]-Ade, 0.18 mM; RNA (34-MER), [U-13C; U-15N]-Gua, 0.19 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	ZfL2-1-34_D2O	isotropic	sample_conditions_1
2D 1H-1H TOCSY	ZfL2-1-34_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	ZfL2-1-34_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	ZfL2-1-34_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC	ZfL2-1-34_H2O	isotropic	sample_conditions_1
2D 1H-13C TROSY	ZfL2-1-34_D2O	isotropic	sample_conditions_1
2D 1H-13C TROSY	ZfL2-1-34_D2O	anisotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CNSSOLVE v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

SPARKY v3.114, Goddard - peak picking

X-PLOR_NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - grid search

NMR spectrometers:

Bruker Avance 600 MHz
Bruker DRX 600 MHz
Bruker Avance 800 MHz