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BMRB: 34324

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

UCAGXCAGU

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

ACUGACUGA

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: 85.4 %, Completeness (bb): 82.4 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	85.4 % (239 of 280)	98.6 % (146 of 148)	67.8 % (78 of 115)	88.2 % (15 of 17)
Suger, PO4	82.4 % (168 of 204)	100.0 % (102 of 102)	60.0 % (51 of 85)	88.2 % (15 of 17)
Nucleobase	93.4 % (71 of 76)	95.7 % (44 of 46)	90.0 % (27 of 30)
Aromatic	92.6 % (63 of 68)	94.7 % (36 of 38)	90.0 % (27 of 30)

1. entity 1

UCAGXCAGU

2. entity 2

ACUGACUGA

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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 pUCAG(PSU)CAGU, 0.5 mM pACUGACUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	pUCAG(PSU)CAGU	natural abundance	0.5 mM
7	pACUGACUGA	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
Deb, I., Popenda, L., Sarzynska, J., Malgowska, M., Lahiri, A., Gdaniec, Z., Kierzek, R.
Sci. Rep. (2019), 9, 16278-16278, PubMed 31700156 , DOI 10.1038/s41598-019-52637-0 , Abstract

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 pUCAG(PSU)CAGU, 0.5 mM pACUGACUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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 303 K, pH 6.8, Details 0.5 mM pUCAG(PSU)CAGU, 0.5 mM pACUGACUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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 pUCAG(PSU)CAGU, 0.5 mM pACUGACUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	pUCAG(PSU)CAGU	natural abundance	0.5 mM
7	pACUGACUGA	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	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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	pUCAG(PSU)CAGU	natural abundance	0.5 mM
2	pACUGACUGA	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	bmr34324_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: bmr34324_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	254		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: 83
  - 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	-4.0
3	A	P	-3.71
4	G	P	-3.86
6	C	P	-3.85
7	A	P	-3.81
8	G	P	-3.93
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	40	63.5
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	26	57.8
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	14	77.8

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	-4.27
3	U	P	-4.23
4	G	P	-3.73
5	A	P	-4.1
6	C	P	-4.2
7	U	P	-4.33
8	G	P	-3.81
9	A	P	-4.04

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	78	100.0
¹³C chemical shifts	61	43	70.5

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	24	100.0
¹³C chemical shifts	16	14	87.5

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 (0.264 seconds)

BMRB: 34324

Sample #1

Sample #2

Experiments performed 8 experiments Detail

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Chemical shift validation 4 contents Detail