BMRB Entry 19040

Name: structure of 2&#039;-5&#039; AG1 lariat forming ribozyme in its inactive state
Published: 2013-04-01

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PDB ID: 2m58
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19040
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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:

structure of 2'-5' AG1 lariat forming ribozyme in its inactive state

Deposition date:

2013-02-18

Original release date:

2013-04-01

Authors:

Carlomagno, Teresa; Amata, Irene; Codutti, Luca; Falb, Melanie; Fohrer, Jorg; Simon, Bernd

Citation:

Citation: Carlomagno, Teresa; Amata, Irene; Codutti, Luca; Falb, Melanie; Fohrer, Jorg; Simon, Bernd. "Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme" J. Am. Chem. Soc. 135, 4403-4411 (2013).
PubMed: 23472843

Assembly members:

Assembly members:
RNA_(59-MER), polymer, 59 residues, 19163.486 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(59-MER): XGAAGAAAGGGCUUCGGCCA CUCAAACUACAGAGACGCCA GUCACUCAGAUAUCCUGGU

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	347
15N chemical shifts	12
1H chemical shifts	430

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) 59 residues - 19163.486 Da.

1

GTP

G

A

G

A

G

2

G

C

U

C

G

C

A

3

C

U

C

A

C

U

A

C

4

A

G

A

G

A

C

G

C

A

5

G

U

C

A

C

U

C

A

G

A

6

U

A

U

C

U

G

U

Samples:

sample_1: ADENOSINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 400 uM; D2O 100%

sample_2: GUANOSINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 300 uM; GUANOSINE-5'-TRIPHOSPHATE, [U-100% 13C; U-100% 15N], 300 uM; D2O 100%

sample_4: CYTIDINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 500 uM; D2O 100%

sample_3: URIDINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 300 uM; D2O 100%

sample_5: ADENOSINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 500 uM; URIDINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 500 uM; D2O 100%

sample_6: ADENOSINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 670 uM; URIDINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 670 uM; CYTIDINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 670 uM; GUANOSINE-5'-MONOPHOSPHATE, [U-100% 13C; U-100% 15N], 670 uM; D2O 100%

sample_7: ADENOSINE-5'-MONOPHOSPHATE 300 uM; URIDINE-5'-MONOPHOSPHATE 300 uM; CYTIDINE-5'-MONOPHOSPHATE 300 uM; GUANOSINE-5'-MONOPHOSPHATE 300 uM; D2O 100%

sample_conditions_1: ionic strength: 0.020 M; pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC ribose	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC base	sample_1	isotropic	sample_conditions_1
2D HNN-COSY	sample_6	isotropic	sample_conditions_1
2D imino NOESY	sample_7	isotropic	sample_conditions_1
3D HsCNb/HbCNb	sample_6	isotropic	sample_conditions_1
3D HCCH-COSY-TOCSY	sample_1	isotropic	sample_conditions_1
3D 13C-edited/ 12C-filtered NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-edited/ 13C-filtered NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC ribose	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC base	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY-TOCSY	sample_2	isotropic	sample_conditions_1
3D 13C-edited/ 12C-filtered NOESY	sample_2	isotropic	sample_conditions_1
3D 13C-edited/ 13C-filtered NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC ribose	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC base	sample_3	isotropic	sample_conditions_1
3D HCCH-COSY-TOCSY	sample_3	isotropic	sample_conditions_1
3D 13C-edited/ 12C-filtered NOESY	sample_3	isotropic	sample_conditions_1
3D 13C-edited/ 13C-filtered NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC ribose	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC base	sample_4	isotropic	sample_conditions_1
3D HCCH-COSY-TOCSY	sample_4	isotropic	sample_conditions_1
3D 13C-edited/ 12C-filtered NOESY	sample_4	isotropic	sample_conditions_1
3D 13C-edited/ 13C-filtered NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC ribose	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC base	sample_5	isotropic	sample_conditions_1
3D HCCH-COSY-TOCSY	sample_5	isotropic	sample_conditions_1
3D 13C-edited/ 12C-filtered NOESY	sample_5	isotropic	sample_conditions_1
3D 13C-edited/ 13C-filtered NOESY	sample_5	isotropic	sample_conditions_1

Software:

FELIX, Accelrys Software Inc. - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz