BMRBj - BMREntryMaster

Found 1 Document (0.334 seconds)

BMRB: 34265

6GE1

Solution structure of the r(UGGUGGU)4 RNA quadruplex

Authors

Andralojc, W., Gdaniec, Z.

Assembly

RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')

Entity

1. RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3') (polymer, Thiol state: not present), 7 monomers, 2317.335 × 4 Da Detail

UGGUGGU

Total weight

9269.34 Da

Max. entity weight

2317.335 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 91.9 %, Completeness (bb): 98.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	91.9 % (102 of 111)	86.4 % (51 of 59)	97.8 % (44 of 45)	100.0 % (7 of 7)
Suger, PO4	98.8 % (83 of 84)	97.6 % (41 of 42)	100.0 % (35 of 35)	100.0 % (7 of 7)
Nucleobase	70.4 % (19 of 27)	58.8 % (10 of 17)	90.0 % (9 of 10)
Aromatic	70.4 % (19 of 27)	58.8 % (10 of 17)	90.0 % (9 of 10)

1. entity 1

UGGUGGU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 bar, Temperature 333 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 333 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	pUGGUGGU	natural abundance	2.0 mM
5	phosphate buffer	natural abundance	10 mM
6	potassium chloride	natural abundance	0.05 mM

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 68.9 %, Completeness (bb): 73.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	68.9 % (153 of 222)	86.4 % (102 of 118)	48.9 % (44 of 90)	50.0 % (7 of 14)
Suger, PO4	73.8 % (124 of 168)	97.6 % (82 of 84)	50.0 % (35 of 70)	50.0 % (7 of 14)
Nucleobase	53.7 % (29 of 54)	58.8 % (20 of 34)	45.0 % (9 of 20)
Aromatic	53.7 % (29 of 54)	58.8 % (20 of 34)	45.0 % (9 of 20)

1. entity 1

UGGUGGU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	pUGGUGGU	natural abundance	2.0 mM
5	phosphate buffer	natural abundance	10 mM
6	potassium chloride	natural abundance	0.05 mM

Chem. Shift Complete3

Sequence coverage: 100.0 %, Completeness: 62.8 %, Completeness (bb): 64.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	³¹P
All	62.8 % (209 of 333)	89.3 % (158 of 177)	32.6 % (44 of 135)	33.3 % (7 of 21)
Suger, PO4	64.7 % (163 of 252)	96.0 % (121 of 126)	33.3 % (35 of 105)	33.3 % (7 of 21)
Nucleobase	56.8 % (46 of 81)	72.5 % (37 of 51)	30.0 % (9 of 30)
Aromatic	56.8 % (46 of 81)	72.5 % (37 of 51)	30.0 % (9 of 30)

1. entity 1

UGGUGGU

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	pUGGUGGU	natural abundance	2.0 mM
5	phosphate buffer	natural abundance	10 mM
6	potassium chloride	natural abundance	0.05 mM

Release date

2018-10-22

Citation

Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus
Andralojc, W., Malgowska, M., Sarzynska, J., Pasternak, K., Szpotkowski, K., Kierzek, R., Gdaniec, Z.
RNA (2018), 25, 121-134, PubMed 30341177 , DOI 10.1261/rna.068163.118 , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

2 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 333 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

3 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	pUGGUGGU	natural abundance	2.0 mM
5	phosphate buffer	natural abundance	10 mM
6	potassium chloride	natural abundance	0.05 mM

4 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	pUGGUGGU	natural abundance	2.0 mM
5	phosphate buffer	natural abundance	10 mM
6	potassium chloride	natural abundance	0.05 mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 333 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

6 2D 1H-31P COSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 333 K, pH 6.8, Details 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
1	pUGGUGGU	natural abundance	2.0 mM
2	phosphate buffer	natural abundance	10 mM
3	potassium chloride	natural abundance	50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_34265_6ge1.nef
Input source #2: Coordindates	6ge1.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	Warning

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

-------
UGGUGGU
|||||||
UGGUGGU

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

-------
UGGUGGU
|||||||
UGGUGGU

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

-------
UGGUGGU
|||||||
UGGUGGU

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

-------
UGGUGGU
|||||||
UGGUGGU

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	7	100.0
B	B	7	100.0
C	C	7	100.0
D	D	7	100.0

Content subtype: combined_34265_6ge1.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	102		100.0 (chain: A, length: 7)
2	Assigned chemical shifts	assigned_chemical_shifts_2	OK	51		100.0 (chain: A, length: 7)
3	Assigned chemical shifts	assigned_chemical_shifts_3	Warning	67		100.0 (chain: A, length: 7)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	96 (96)	.	100.0 (chain: A, length: 7), 100.0 (chain: B, length: 7), 100.0 (chain: C, length: 7), 100.0 (chain: D, length: 7)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 51
  - ¹³C chemical shifts: 44
  - ³¹P chemical shifts: 7
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 51
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 67
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	U	P	-1.237
2	G	P	-4.322
3	G	P	-2.22
4	U	P	-3.401
5	G	P	-5.103
6	G	P	-3.945
7	U	P	-3.13

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	51	86.4
¹³C chemical shifts	45	44	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	41	97.6
¹³C chemical shifts	35	35	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	10	58.8
¹³C chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	51	86.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	41	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	10	58.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	H21	9.869
2	G	H22	6.925
3	G	H21	9.729
4	U	HO2'	6.867
5	G	H21	10.075
5	G	H22	6.132
5	G	HO2'	6.731
6	G	H21	9.625
6	G	H22	7.429
6	G	HO2'	6.74
7	U	HO2'	7.077

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	56	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	39	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 7, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 7, Sequence coverage: 100.0%
- Total number of restraints: 96
- Total number of restraints per polymer type: 96
- Weight of restraints: 1.0 (96)
- Potential type of restraints: square-well-parabolic (96)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

Keywords RNA, U-tetrad, parallel stranded, quadruplex, tetramolecular

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Found 1 Document (0.334 seconds)

BMRB: 34265

Sample #1

Sample #2

Sample #1

Sample #2

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail