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BMRB: 15781

2K41

NMR structure of uridine bulged RNA duplex

Authors

Popenda, L., Bielecki, L., Gdaniec, Z., Adamiak, R.W.

Assembly

5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3'

Entity

1. RNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3') (polymer, Thiol state: not present), 9 monomers, 2927.699 Da Detail

GUCGUGCUG

2. RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') (polymer, Thiol state: not present), 8 monomers, 2587.565 Da Detail

CAGCCGAC

Total weight

5515.2637 Da

Max. entity weight

2927.699 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.2 %, Completeness (bb): 97.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	97.2 % (273 of 281)	98.0 % (148 of 151)	97.3 % (110 of 113)	88.2 % (15 of 17)
Suger, PO4	97.5 % (199 of 204)	100.0 % (102 of 102)	96.5 % (82 of 85)	88.2 % (15 of 17)
Nucleobase	96.1 % (74 of 77)	93.9 % (46 of 49)	100.0 % (28 of 28)
Aromatic	95.4 % (62 of 65)	91.9 % (34 of 37)	100.0 % (28 of 28)

1. RNA (5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3')

GUCGUGCUG

2. RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')

CAGCCGAC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
8	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
9	NaCl			50 mM
10	phosphate buffer			10 mM
11	EDTA			0.1 mM
12	H2O	natural abundance		90 %
13	D2O			10 %

Release date

2008-09-01

Citation

Bulged adenosine influence on the RNA duplex conformation in solution
Popenda, L., Adamiak, R.W., Gdaniec, Z.
Biochemistry (2008), 47, 5059-5067, PubMed 18399645 , DOI 10.1021/bi7024904 , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

2 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

5 2D 1H-31P HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
2	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
3	NaCl			50 mM
4	phosphate buffer			10 mM
5	EDTA			0.1 mM
6	D2O			100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	RNA (5'-R(GPUPCPGPUPGPCPUP*G)-3')	natural abundance		1 mM
8	RNA (5'-R(CPAPGPCPCPGPAPC)-3')	natural abundance		1 mM
9	NaCl			50 mM
10	phosphate buffer			10 mM
11	EDTA			0.1 mM
12	H2O	natural abundance		90 %
13	D2O			10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15781_2k41.nef
Input source #2: Coordindates	2k41.cif
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	Error

Disulfide bonds

None

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---------
GUCGUGCUG
|||||||||
GUCGUGCUG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

10------
CAGCCGAC
||||||||
CAGCCGAC
--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	9	0	0	100.0
B	B	8	0	0	100.0

Content subtype: combined_15781_2k41.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	232		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	275 (1)	noe	100.0 (chain: A, length: 9), 100.0 (chain: B, length: 8)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 8, Sequence coverage: 100.0%
- Total number of restraints: 275
- Weight of restraints: 1.0 (275)
- Potential type of restraints: square-well-parabolic (275)
- Range of distance target values: 1.93, 5.25 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords duplex, NMR, RNA, uridine bulge