BMRB Entry 18593

Name: Solution Structure of a RNA Duplex Containing a 2&#039;-O-Pivaloyloxymethyl Modification
Published: 2015-07-24

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PDB ID: 2lvy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18593
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:

Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification

Deposition date:

2012-07-13

Original release date:

2015-07-24

Authors:

Baraguey, Carine

Citation:

Citation: Baraguey, Carine; Lescrinier, Eveline; Lavergne, Thomas; Debart, Francoise; Herdewijn, Piet; Vasseur, Jean-Jacques. "The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure" Org. Biomol. Chem. 11, 2638-2647 (2013).
PubMed: 23455628

Assembly members:

Assembly members:
modified_strand, polymer, 9 residues, 2499.596 Da.
non-modified_complementary_strand, polymer, 9 residues, 2885.813 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
modified_strand: CGCXACGCT
non-modified_complementary_strand: GCGUAGCGT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	178

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA/RNA (5'-R(CPGPCP(UPV)APCPGPC)-D(PT)-3')	1
2	DNA/RNA (5'-R(GPCPGPUPAPCPGPC)-D(PT)-3')	2

Entities:

Entity 1, DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 9 residues - 2499.596 Da.

Residues 1-8 are riboses. Residue 9 is an overhanging deoxythymidine.

1

C

G

C

UPV

A

C

G

C

DT

Entity 2, DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 9 residues - 2885.813 Da.

Residues 10-17 are riboses. Residue 18 is an overhanging deoxythymidine.

1

G

C

G

U

A

G

C

G

DT

Samples:

sample_1: DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 0.9 mM; DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 0.9 mM

sample_2: DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3') 0.9 mM; DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3') 0.9 mM

sample_conditions_1: ionic strength: 0 M; pH: 6.7; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 0 M; pH: 6.7; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P HETCOR	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

X-PLOR NIH v2.25, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz