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Found 1 Document (0.351 seconds)

BMRB: 34323

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

Authors

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

Assembly

RNA duplex containing pseudouridine residue

Entity

1. RNA duplex containing pseudouridine residue, entity 1 (polymer, Thiol state: not present), 9 monomers, 2895.699 Da Detail

UCACXGAGU

2. RNA duplex containing pseudouridine residue, entity 2 (polymer, Thiol state: not present), 9 monomers, 2918.739 Da Detail

ACUCAGUGA

Total weight

5814.438 Da

Max. entity weight

2918.739 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 87.9 %, Completeness (bb): 84.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	87.9 % (246 of 280)	98.6 % (146 of 148)	73.9 % (85 of 115)	88.2 % (15 of 17)
Suger, PO4	84.3 % (172 of 204)	100.0 % (102 of 102)	64.7 % (55 of 85)	88.2 % (15 of 17)
Nucleobase	97.4 % (74 of 76)	95.7 % (44 of 46)	100.0 % (30 of 30)
Aromatic	97.1 % (66 of 68)	94.7 % (36 of 38)	100.0 % (30 of 30)

1. entity 1

UCACXGAGU

2. entity 2

ACUCAGUGA

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	pUCAC(PSU)GAGU	natural abundance	0.5 mM
7	pACUCAGUGA	natural abundance	0.5 mM
8	sodium phosphate	natural abundance	10 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	0.1 mM

Release date

2019-11-10

Citation

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair
Gdaniec, Z., Deb, I., Popenda, L., Sarzynska, J., Malgowska, M., Lahiri, A., Kierzek, R.
Sci. Rep. (2019), 9, 16278-16278, PubMed 31700156 , DOI 10.1038/s41598-019-52637-0 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34324 released on 2019-11-10
Title Structure of the RNA duplex containing pseudouridine residue (5'-Gp(PSU)pC-3' sequence context)

Experiments performed 8 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.8, Details 0.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

3 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details 0.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	pUCAC(PSU)GAGU	natural abundance	0.5 mM
7	pACUCAGUGA	natural abundance	0.5 mM
8	sodium phosphate	natural abundance	10 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	0.1 mM

4 2D DQF-COSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

5 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

7 2D 1H-31P COSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

8 2D 1H-31P hetero TOCSY-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pUCAC(PSU)GAGU	natural abundance	0.5 mM
2	pACUCAGUGA	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	150 mM
5	EDTA	natural abundance	0.1 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34323_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	5	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts

Content subtype: bmr34323_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	261		100.0 (chain: 1, length: 9), 100.0 (chain: 2, length: 9)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 9, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 155
  - ¹³C chemical shifts: 90
  - ³¹P chemical shifts: 16
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	C	P	-3.91
3	A	P	-3.85
4	C	P	-4.04
6	G	P	-3.61
7	A	P	-3.85
8	G	P	-3.9
9	U	P	-4.31

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	77	93.9
¹³C chemical shifts	63	44	69.8
³¹P chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	54	98.2
¹³C chemical shifts	45	29	64.4
³¹P chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	23	85.2
¹³C chemical shifts	18	15	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	C	P	-4.15
3	U	P	-4.36
4	C	P	-3.98
5	A	P	-3.77
6	G	P	-3.91
7	U	P	-4.5
8	G	P	-3.73
9	A	P	-4.01

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	78	100.0
¹³C chemical shifts	61	46	75.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	54	100.0
¹³C chemical shifts	45	30	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	8	100.0

Keywords RNA, duplex, pseudouridine

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Found 1 Document (0.351 seconds)

BMRB: 34323

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 4 contents Detail