BMRB Entry 17860

Name: high resolution NMR solution structure of helix H1 of the chimpanzee HAR1 RNA
Published: 2012-07-24

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PDB ID: 2lhp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17860
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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:

high resolution NMR solution structure of helix H1 of the chimpanzee HAR1 RNA

Deposition date:

2011-08-12

Original release date:

2012-07-24

Authors:

Cevec, Mirko; Ziegeler, Melanie; Richter, Christian; Schwalbe, Harald

Citation:

Citation: Ziegeler, Melanie; Cevec, Mirko; Richter, Christian; Schwalbe, Harald. "NMR Studies of HAR1 RNA Secondary Structures Reveal Conformational Dynamics in the Human RNA" Chembiochem 13, 2100-2112 (2012).
PubMed: 22961937

Assembly members:

Assembly members:
RNA_(37-MER), polymer, 37 residues, 11872.162 Da.

Natural source:

Natural source: Common Name: chimpanzee Taxonomy ID: 9598 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Pan troglodytes

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: Escherichia coli Vector: pUC19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(37-MER): GGGUGAAAUGGAGGACUUCG GUCCUCAAAUUUCACCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	282

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (37-MER)	1

Entities:

Entity 1, RNA (37-MER) 37 residues - 11872.162 Da.

1

G

U

G

A

U

G

2

G

A

G

A

C

U

C

G

3

G

U

C

U

C

A

U

4

U

C

A

C

Samples:

sample_1: RNA (37-MER) 0.6 mM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_2: RNA (37-MER), [U-100% 15N], 0.4 mM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_3: RNA (37-MER), [U-13C; U-15N]-Ade,Ura, 0.3 mM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_4: RNA (37-MER), [U-13C; U-15N]-Cyt,Gua, 1 mM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_5: RNA (37-MER), [U-13C; U-15N]-Cyt,Gua, 1 mM; potassium chloride 50 mM; potassium phosphate 25 mM

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
2D HNN-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
3D 1H-13C-13C-TROSY relayed HCCH-COSY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_5	isotropic	sample_conditions_2
2D 1H-13C HCCNH-TOCSY	sample_3	isotropic	sample_conditions_2
3D HCP	sample_5	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_5	isotropic	sample_conditions_1
3D forward-directed HCC-TOCSY-CCH E.COSY	sample_5	isotropic	sample_conditions_1
2D H(C)N	sample_5	isotropic	sample_conditions_1
2D HNCO	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_1

Software:

ARIA v1.2, Linge, O'Donoghue and Nilges - refinement

TOPSPIN v2.1, Bruker Biospin - collection, processing

SPARKY v3.113, Goddard - data analysis

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 950 MHz
Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz