BMRB Entry 18838

Name: Solution structure of the ID3 stem loop of domain 1 in the ai5gamma group II intron
Published: 2013-10-21

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PDB ID: 2m12
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18838
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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 the ID3 stem loop of domain 1 in the ai5gamma group II intron

Deposition date:

2012-11-13

Original release date:

2013-10-21

Authors:

Popovic, Milena; Greenbaum, Nancy

Citation:

Citation: Popovic, Milena; Greenbaum, Nancy. "Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site." RNA 20, 24-35 (2014).
PubMed: 24243113

Assembly members:

Assembly members:
ID3, polymer, 23 residues, 132.116 Da.

Natural source:

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Host organism: Saccharomyces cerevisiae

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ID3: GGGUGUAUUGGAAAUGAGCA CCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	132
1H chemical shifts	158

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ID3 stem loop	1

Entities:

Entity 1, ID3 stem loop 23 residues - 132.116 Da.

1

G

U

G

U

A

U

G

2

G

A

U

G

A

G

C

A

3

C

Samples:

sample_1: ID30.03 – 0.9 mM; sodium chloride 60 mM; H2O 90%; D2O 10%

sample_2: ID30.03 – 0.9 mM; sodium chloride 60 mM; D2O 100%

sample_3: ID3, [U-100% 13C; U-100% 15N], 0.3 – 0.5 mM; sodium chloride 60 mM; H2O 90%; D2O 10%

sample_4: ID3, [U-100% 13C; U-100% 15N], 0.3 – 0.5 mM; potassium chloride 60 mM; D2O 100%

sample_conditions_1: ionic strength: 0.06 M; pH: 6.4; pressure: 1 atm; temperature: 277 K

sample_conditions_2: ionic strength: 0.06 M; pH: 6.4; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_4	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_2
3D HCCH-COSY	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CCPN, CCPN - chemical shift assignment

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance 600 MHz