BMRB Entry 16980

Name: RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width
Published: 2010-07-26

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PDB ID: 2kyd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16980
MolProbity Validation Chart

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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:

RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width

Deposition date:

2010-06-07

Original release date:

2010-07-26

Authors:

Tolbert, Blanton; Summers, Michael; Miyazaki, Yasuyuki; Barton, Shawn; Kinde, Benyam; Stark, Patrice; Singh, Rashmi; Bax, Ad; Case, David

Citation:

Citation: Tolbert, Blanton; Miyazaki, Yasuyuki; Barton, Shawn; Kinde, Benyam; Starck, Patrice; Singh, Rashmi; Bax, Ad; Case, David; Summers, Michael. "Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement." J. Biomol. NMR 47, 205-219 (2010).
PubMed: 20549304

Assembly members:

Assembly members:
RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3'), polymer, 29 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Murine leukemia virus Taxonomy ID: 11786 Superkingdom: not available Kingdom: not available Genus/species: Gammaretrovirus not available

Experimental source:

Experimental source: Production method: cell free synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3'): GCGGUACUAGUUAGCUAACU AGCUUUGUA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	77

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')_1	1
2	RNA (5'-R(CPUPAPGPUPUPAPGPCPUPAPAPCPUPAPG)-3')_2	1

Entities:

Entity 1, RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3')_1 29 residues - Formula weight is not available

1

G

C

G

U

A

C

U

A

G

2

U

A

G

C

U

A

C

U

3

A

G

C

U

G

U

A

Samples:

slb1: RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3')0.25 – 1 mM; RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3'), [U-100% 13C], [C-100% 13C], 0.25 mM; RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3'), [G-100% 13C], [A-100% 13C], 0.25 mM; sodium chloride 150 mM; TRIS 10 mM; D2O 100%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	slb1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	slb1	isotropic	sample_conditions_1
2D 1H-13C HMQC	slb1	isotropic	sample_conditions_1
2D Tr 1H-13C HSQC	slb1	isotropic	sample_conditions_1
2D Tr 1H-13C HSQC	slb1	anisotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization

NMR spectrometers:

Bruker Avance 800 MHz
Bruker DMX 600 MHz