BMRB Entry 18881

Name: NMR solution structure of the d3&#039;-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid
Published: 2014-06-09

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PDB ID: 2m1v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18881
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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:

NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

Deposition date:

2012-12-07

Original release date:

2014-06-09

Authors:

Skilandat, Miriam; Sigel, Roland

Citation:

Citation: Skilandat, Miriam; Sigel, Roland. "Determinants of DNA cleavage site recognition in group II intron retrohoming - Solution structure and metal-ion binding sites of the Sc.ai5gamma RNA:DNA contact" .

Assembly members:

Assembly members:
RNA_(29-MER), polymer, 29 residues, 9301.611 Da.
DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3'), polymer, 7 residues, 2113.428 Da.

Natural source:

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: not available Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(29-MER): GGAGUAUGUAUUGGCACUGA GCAUACUCC
DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3'): CAGTGTC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	56
15N chemical shifts	41
1H chemical shifts	288

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (29-MER)	1
2	DNA_(5'-D(CPAPGPTPGPTP*C)-3')	2

Entities:

Entity 1, RNA (29-MER) 29 residues - 9301.611 Da.

1

G

A

G

U

A

U

G

U

A

2

U

G

C

A

C

U

G

A

3

G

C

A

U

A

C

U

C

Entity 2, DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3') 7 residues - 2113.428 Da.

1

DC

DA

DG

DT

DG

DT

DC

Samples:

sample_1: RNA_(29-MER)0.6 – 0.9 mM; DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')0.7 – 1.0 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 100%

sample_2: RNA_(29-MER)0.6 – 0.9 mM; DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')0.7 – 1.0 mM; potassium chloride 110 mM; EDTA 10 uM; H2O 90%; D2O 10%

sample_3: RNA_(29-MER), [U-100% 13C; U-100% 15N], 0.6 – 0.9 mM; DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')0.7 – 1.0 mM; potassium chloride 110 mM; EDTA 10 uM; H2O 90%; D2O 10%

sample_4: RNA_(29-MER)0.5 – 1.0 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 100%

sample_5: RNA_(29-MER), [3',4',5',5'',5]-100% 2H, 0.6 – 0.9 mM; DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3') 0.7-1.0 mM; potassium chloride 110 mM; EDTA 10 uM

sample_6: RNA_(29-MER), [U-100% 13C; U-100% 15N], 0.6 – 0.9 mM; DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')0.7 – 1.0 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 100%

sample_7: RNA_(29-MER), [U-100% 13C; U-100% 15N], 0.5 – 1.0 mM; potassium chloride 10 mM; EDTA 10 uM; H2O 90%; D2O 10%

sample_8: RNA (29-MER)0.5 – 1.0 mM; potassium chloride 10 mM; EDTA 10 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 110 mM; pD: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

sample_conditions_4: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC aliphatic	sample_6	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_6	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC aliphatic	sample_6	anisotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_6	anisotropic	sample_conditions_1
1D 31P	sample_1	isotropic	sample_conditions_1
F1, F2 X-filtered 1H-1H NOESY	sample_3	isotropic	sample_conditions_2
F1, F2 X-filtered 1H-1H TOCSY	sample_3	isotropic	sample_conditions_2

Software:

TOPSPIN v3.0, Bruker Biospin - data analysis, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

DYANA v1.5, Guntert, Braun and Wuthrich - data analysis, structure solution

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

X-PLOR NIH v2.3, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz