BMRB Entry 34324

Name: Structure of the RNA duplex containing pseudouridine residue (5&#039;-Gp(PSU)pC-3&#039; sequence context)
Published: 2019-11-12

Click here to enlarge.

PDB ID: 6i1w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34324
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context)

Deposition date:

2018-10-30

Original release date:

2019-11-12

Authors:

Deb, I.; Popenda, L.; Sarzynska, J.; Gdaniec, Z.

Citation:

Citation: Deb, I.; Popenda, L.; Sarzynska, J.; Malgowska, M.; Lahiri, A.; Gdaniec, Z.; Kierzek, R.. "Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair." Sci. Rep. 9, 16278-16278 (2019).
PubMed: 31700156

Assembly members:

Assembly members:
entity_1, polymer, 9 residues, 2832.727 Da.
entity_2, polymer, 9 residues, 2855.767 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 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):
entity_1: UCAGXCAGU
entity_2: ACUGACUGA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	83
1H chemical shifts	155
31P chemical shifts	16

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 9 residues - 2832.727 Da.

1

U

C

A

G

PSU

C

A

G

U

Entity 2, entity_2 9 residues - 2855.767 Da.

1

A

C

U

G

A

C

U

G

A

Samples:

sample_1: pUCAG(PSU)CAGU 0.5 mM; pACUGACUGA 0.5 mM; sodium phosphate 10 mM; sodium chloride 150 mM; EDTA 0.1 mM

sample_2: pUCAG(PSU)CAGU 0.5 mM; pACUGACUGA 0.5 mM; sodium phosphate 10 mM; sodium chloride 150 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0.16 M; pH: 6.8; pressure: 1 atm; temperature: 288 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_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_1
2D 1H-31P hetero TOCSY-NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

Felix, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE III 700 MHz