BMRB Entry 19545

Name: The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03
Published: 2014-10-13

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PDB ID: 2mfd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19545
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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:

The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03

Deposition date:

2013-10-11

Original release date:

2014-10-13

Authors:

Ihle, Yvonne; Zell, Roland; Gorlach, Matthias

Citation:

Citation: Ihle, Yvonne; Zell, Roland; Gorlach, Matthias. "The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir 404/03" .

Assembly members:

Assembly members:
BEVSLD5, polymer, 19 residues, 6070.675 Da.

Natural source:

Natural source: Common Name: bovine enterovirus Taxonomy ID: 12064 Superkingdom: Viruses Kingdom: not available Genus/species: Enterovirus E

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
BEVSLD5: GGCGUUCGCUUAGAACGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	132
15N chemical shifts	17
1H chemical shifts	190

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(PGPGPCPGPUPUPCPGPCPUPUPAPGPAPAPCPGPUP*C)-3')	1

Entities:

Entity 1, RNA (5'-R(P*GP*GP*CP*GP*UP*UP*CP*GP*CP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C)-3') 19 residues - 6070.675 Da.

Residues 55-57 and 71-73 are non-native and were attached facilitating transcription and purification.

1

G

C

G

U

C

G

C

U

2

U

A

G

A

C

G

U

C

Samples:

unl-BEVSLD5: BEVSLD5 1.1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 0.2 mM; H2O 90%; D2O 10%

BEVSLD5_1: BEVSLD5, [U-100% 13C; U-100% 15N], 0.9 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 0.2 mM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aliphatic	unl-BEVSLD5	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	unl-BEVSLD5	isotropic	sample_conditions_1
2D 1H-1H COSY	unl-BEVSLD5	isotropic	sample_conditions_1
2D 1H-1H NOESY	unl-BEVSLD5	isotropic	sample_conditions_1
2D DQF-COSY	unl-BEVSLD5	isotropic	sample_conditions_1
2D 1H-1H TOCSY	unl-BEVSLD5	isotropic	sample_conditions_1
2D HcncH + 2D HccH-COSY	BEVSLD5_1	isotropic	sample_conditions_1
2D HcnH + 2D HccH-TOCSY	BEVSLD5_1	isotropic	sample_conditions_1
3D HCCH-COSY	BEVSLD5_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	BEVSLD5_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	BEVSLD5_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	unl-BEVSLD5	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	BEVSLD5_1	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	BEVSLD5_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	unl-BEVSLD5	isotropic	sample_conditions_2

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA v1.5.5, Rochus Keller - chemical shift assignment, peak picking

CYANA v1.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 750 MHz