BMRB Entry 26024

Name: RNA Bulge Loop that Specifically Binds Metal Ions
Published: 2016-09-22

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PDB ID: 2nci
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26024
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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:

RNA Bulge Loop that Specifically Binds Metal Ions

Deposition date:

2016-04-08

Original release date:

2016-09-22

Authors:

Gu, Xiaobo; Schroeder, Susan

Citation:

Citation: Gu, Xiaobo; Park, Sun-Young; Tonelli, Marco; Cornilescu, Gabriel; Xia, Tianbing; Zhong, Dongping; Schroeder, Susan. "NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions" J. Phys. Chem. Lett. ., 3841-3846 (2016).
PubMed: 27631837

Assembly members:

Assembly members:
RNA_(28-MER), polymer, 28 residues, 8970.434 Da.

Natural source:

Natural source: Common Name: bacteriophage Taxonomy ID: 38018 Superkingdom: Viruses Kingdom: not available Genus/species: not available unidentified phage

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Host organism: Transcription of RNA using T7 polymerase Vector: Transcription of RNA using T7 polymerase

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(28-MER): GGACGUUAAAAGGCUUCGGC CUACGUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	78
15N chemical shifts	11
1H chemical shifts	184

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (28-MER)	1

Entities:

Entity 1, RNA (28-MER) 28 residues - 8970.434 Da.

1

G

A

C

G

U

A

2

A

G

C

U

C

G

C

3

C

U

A

C

G

U

C

Samples:

AU_label: RNA (28-MER), [U-98% 13C; U-98% 15N]-A,U, 1.5 mM; cobalt hexamine 1.5 mM; sodium chloride 10 mM; sodium phosphate 10 mM

NO_label: RNA (28-MER) 1 mM; cobalt hexamine 1 mM; sodium chloride 10 mM; sodium phosphate 10 mM

AU_label_RDC: RNA (28-MER), [U-98% 13C; U-98% 15N]-A,U, 1.5 mM; cobalt hexamine 1.5 mM; phage 5 mg/mL; sodium chloride 10 mM; sodium phosphate 10 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 20 mM; pH: 6; pressure: 1 bar; temperature: 274 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	AU_label	isotropic	sample_conditions_1
3D HCCH-TOCSY	AU_label	isotropic	sample_conditions_1
2D NOESY13CHSQC	AU_label	isotropic	sample_conditions_1
2D HCNTROSY	AU_label	isotropic	sample_conditions_1
2D NOESY	AU_label	isotropic	sample_conditions_1
2D 1H-13C HSQC	AU_label_RDC	isotropic	sample_conditions_1
2D NOESY	NO_label	isotropic	sample_conditions_2
2D COSY	NO_label	isotropic	sample_conditions_2
2D 1H-13C HSQC	NO_label	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Varian VNMRS 500 MHz
Agilent INOVA 900 MHz
Agilent INOVA 800 MHz
Agilent NMR System 600 MHz