BMRB Entry 18950

Name: THE SOLUTION STRUCTURE OF 3&#039;,5&#039;-LINKED 2&#039;-O-(2-METHOXYETHYL)-RNA DUPLEX
Published: 2013-11-26

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PDB ID: 2m39
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18950
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:

THE SOLUTION STRUCTURE OF 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX

Deposition date:

2013-01-15

Original release date:

2013-11-26

Authors:

Plevnik, Miha; Cevec, Mirko; Plavec, Janez

Citation:

Citation: Plevnik, Miha; Cevec, Mirko; Plavec, Janez. "NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex." Biochimie 95, 2385-2391 (2013).
PubMed: 24012551

Assembly members:

Assembly members:
5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', polymer, 12 residues, 1889.457 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):
5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3': XXXXXXXXXXXG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	173

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(P(G48)P(A44)P(A44)P(T39)P*(T39))-3')_1	1
2	RNA (5'-R(P(G48)P(A44)P(A44)P(T39)P*(T39))-3')_2	1

Entities:

Entity 1, RNA (5'-R(P*(G48)P*(A44)P*(A44)P*(T39)P*(T39))-3')_1 12 residues - 1889.457 Da.

1

C5L

G48

C5L

G48

A44

T39

C5L

G48

2

C5L

DG

Samples:

sample_1: 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 2.5 mM; potassium chloride 100 mM

sample_2: 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 2.5 mM; potassium chloride 100 mM

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2

Software:

VNMR v6.1B, Varian - collection, processing

FELIX v2000, Accelrys Software Inc. - processing

AMBER v7, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

NMR spectrometers:

Varian Unity Inova 600 MHz