BMRBj - BMREntryMaster

Found 1 Document (0.27 seconds)

BMRB: 34676

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene

Authors

Wang, Z., Jurt, S., Dominguez-Martin, A., Johannsen, S., Sigel, R.K.O.

Assembly

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

Entity

1. RNA (5'-R(*GP*GP*GP*CP*CP*AP*UP*AP*GP*GP*GP*UP*GP*GP*GP*AP*UP*CP*UP*GP*GP*G)-3') (polymer, Thiol state: not present), 22 monomers, 7288.309 Da Detail

GGGCCAUAGG GUGGGAUCUG GG

Formula weight

7288.309 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.4 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	92.4 % (318 of 344)	94.6 % (176 of 186)	100.0 % (142 of 142)	0.0 % (0 of 16)
Suger, PO4	100.0 % (242 of 242)	100.0 % (132 of 132)	100.0 % (110 of 110)
Nucleobase	74.5 % (76 of 102)	81.5 % (44 of 54)	100.0 % (32 of 32)	0.0 % (0 of 16)
Aromatic	79.2 % (76 of 96)	91.7 % (44 of 48)	100.0 % (32 of 32)	0.0 % (0 of 16)

1. entity 1

GGGCCAUAGG GUGGGAUCUG GG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BCL-2 6A8A17U	natural abundance		1.3 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	BCL-2 6A8A17U	natural abundance		1.3 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM G 15N-labeled BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	BCL-2 6A8A17U	[G 15N-labeled]		0.5 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM A 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	BCL-2 6A8A17U	[A 13C, 15N-labeled]		0.3 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM C 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	BCL-2 6A8A17U	[C 13C, 15N-labeled]		0.3 mM

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM G 13C-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	BCL-2 6A8A17U	[G 13C-labeled]		0.5 mM

Sample #7

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM U 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	BCL-2 6A8A17U	[U 13C, 15N-labeled]		0.3 mM

Release date

2021-12-05

Citation

Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
Wang, Z., Jurt, S., Dominguez-Martin, A., Johannsen, S., Sigel, R.K.O.

Experiments performed 12 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BCL-2 6A8A17U	natural abundance		1.3 mM

2 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	BCL-2 6A8A17U	natural abundance		1.3 mM

3 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	BCL-2 6A8A17U	natural abundance		1.3 mM

4 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	BCL-2 6A8A17U	natural abundance		1.3 mM

5 JR-HMBC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	BCL-2 6A8A17U	natural abundance		1.3 mM

6 H8N2 HNN-COSY

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM G 15N-labeled BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	BCL-2 6A8A17U	[G 15N-labeled]		0.5 mM

7 H1N2 HNN-COSY

Instrument

Bruker AVANCE - 700 MHz Cryo-TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM G 15N-labeled BCL-2 6A8A17U, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	BCL-2 6A8A17U	[G 15N-labeled]		0.5 mM

8 H1pC6/8 HMBC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.3 mM BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	BCL-2 6A8A17U	natural abundance		1.3 mM

9 constant-time 1H-13C HSQC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM A 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	BCL-2 6A8A17U	[A 13C, 15N-labeled]		0.3 mM

10 constant-time 1H-13C HSQC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM C 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	BCL-2 6A8A17U	[C 13C, 15N-labeled]		0.3 mM

11 constant-time 1H-13C HSQC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.5 mM G 13C-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	BCL-2 6A8A17U	[G 13C-labeled]		0.5 mM

12 constant-time 1H-13C HSQC

Instrument

Bruker AVANCE - 600 MHz Cryo-TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3 mM U 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	BCL-2 6A8A17U	[U 13C, 15N-labeled]		0.3 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34676_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

None

Content subtype: bmr34676_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	378		100.0 (chain: 1, length: 22)
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: 22, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 184
- ¹³C chemical shifts: 182
- ¹⁵N chemical shifts: 12

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	C4	154.148
1	G	C5	118.552
1	G	N2	80.376
2	G	H21	9.821
2	G	H22	5.854
2	G	C4	153.531
2	G	C5	118.018
2	G	N2	82.299
3	G	C4	153.988
3	G	C5	117.507
3	G	N2	81.771
4	C	C2	159.641
5	C	C2	160.096
6	A	C4	151.482
6	A	C5	121.446
6	A	C6	158.123
7	U	C2	154.396
8	A	C4	151.738
8	A	C5	121.654
8	A	C6	157.898
9	G	C4	154.346
9	G	C5	118.315
9	G	N2	80.925
10	G	H21	9.362
10	G	H22	6.873
10	G	C4	154.576
10	G	C5	117.897
10	G	N2	82.782
11	G	C4	155.463
11	G	C5	116.916
11	G	N2	82.58
12	U	C2	154.911
13	G	C4	153.153
13	G	C5	119.294
13	G	N2	80.303
14	G	H21	9.582
14	G	H22	6.032
14	G	C4	153.767
14	G	C5	117.919
14	G	N2	81.883
15	G	C4	154.212
15	G	C5	117.233
15	G	N2	82.434
16	A	C4	151.799
16	A	C5	121.752
16	A	C6	158.219
17	U	C2	154.471
18	C	C2	160.004
19	U	C2	154.307
20	G	C4	154.194
20	G	C5	118.589
20	G	N2	80.43
21	G	H21	9.715
21	G	H22	5.957
21	G	C4	153.78
21	G	C5	117.965
21	G	N2	82.102
22	G	C4	154.056
22	G	C5	117.44
22	G	N2	82.193

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	186	176	94.6
¹³C chemical shifts	142	142	100.0
¹⁵N chemical shifts	16	0	0.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	132	100.0
¹³C chemical shifts	110	110	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	44	81.5
¹³C chemical shifts	32	32	100.0
¹⁵N chemical shifts	16	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	18	100.0

Histogram of normalized assigned chemical shifts

Keywords 5'UTR, BCL-2, G-quadruplex, RNA, intramolecular, mRNA

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Found 1 Document (0.27 seconds)

BMRB: 34676

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Experiments performed 12 experiments Detail

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Chemical shift validation 3 contents Detail