BMRBj - BMREntryMaster

Found 1 Document (0.319 seconds)

BMRB: 28081

Trimolecular G-quadruplex

Authors

Jing, H., Fu, W., Zhang, N.

Assembly

Trimolecular G-quadruplex

Entity

1. Trimolecular G-quadruplex (polymer, Thiol state: not present), 18 monomers, 5745.643 × 3 Da Detail

GTTAGGGTTA GGGTTAGG

Total weight

17236.93 Da

Max. entity weight

5745.643 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete1

Sequence coverage: 94.4 %, Completeness: 77.4 %, Completeness (bb): 76.2 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	77.4 % (130 of 168)	77.4 % (130 of 168)
Suger, PO4	76.2 % (96 of 126)	76.2 % (96 of 126)
Nucleobase	81.0 % (34 of 42)	81.0 % (34 of 42)
Aromatic	77.8 % (28 of 36)	77.8 % (28 of 36)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. Trimolecular G-quadruplex

GTTAGGGTTA GGGTTAGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Trimolecular G-quadruplex	natural abundance	8 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	[U-99% 2H]	10 %
5	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	Trimolecular G-quadruplex	natural abundance	8 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-99% 2H]	100 %

Chem. Shift Complete2

Sequence coverage: 16.7 %, Completeness: 44.0 %, Completeness (bb): 44.0 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	44.0 % (148 of 336)	44.0 % (148 of 336)
Suger, PO4	44.0 % (111 of 252)	44.0 % (111 of 252)
Nucleobase	44.0 % (37 of 84)	44.0 % (37 of 84)
Aromatic	43.1 % (31 of 72)	43.1 % (31 of 72)
Methyl	50.0 % (6 of 12)	50.0 % (6 of 12)

1. Trimolecular G-quadruplex

GTTAGGGTTA GGGTTAGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Trimolecular G-quadruplex	natural abundance	8 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	[U-99% 2H]	10 %
5	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8

#	Name	Isotope labeling	Concentration
6	Trimolecular G-quadruplex	natural abundance	8 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-99% 2H]	100 %

Release date

2020-02-16

Citation

NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance
Jing, H., Fu, W., Hu, W., Xu, S., Xu, X., He, M., Liu, Y., Zhang, N.
Nucleic Acids Res. (2021), 49, 2306-2316, PubMed 33524157 , DOI 10.1093/nar/gkab028 , Abstract

Related entities 1. Trimolecular G-quadruplex, : 1 entities Detail

Experiments performed 4 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr28081_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: bmr28081_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	167	100.0 (chain: 1, length: 18)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	36	100.0 (chain: 1, length: 18)
1	Chemical shift references	chemical_shift_reference_1	OK	1	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 167

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	H21	6.3
1	DG	H22	9.89
5	DG	H21	7.16
5	DG	H22	9.74
6	DG	H21	6.89
6	DG	H22	9.89
7	DG	H21	6.08
7	DG	H22	9.83
11	DG	H21	7.0
11	DG	H22	9.41
12	DG	H21	6.66
12	DG	H22	10.0
17	DG	H21	7.17
17	DG	H22	9.03
18	DG	H21	6.64
18	DG	H22	9.77

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	139	82.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	103	81.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	36	85.7

Methyl group atoms

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

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0

Histogram of normalized assigned chemical shifts

Saveframe: assigned_chem_shift_list_2

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
Total number of assignments
- ¹³C chemical shifts: 27
- ¹⁵N chemical shifts: 9

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C8	138.14
1	DG	N1	144.56
2	DT	C6	140.09
2	DT	C7	14.51
3	DT	C6	138.21
3	DT	C7	14.86
3	DT	N3	160.84
4	DA	C2	154.63
4	DA	C8	141.03
5	DG	C8	141.73
5	DG	N1	145.05
6	DG	C8	139.39
6	DG	N1	145.13
7	DG	C8	138.06
7	DG	N1	144.67
8	DT	C6	138.99
8	DT	C7	14.49
9	DT	C6	139.29
9	DT	C7	14.7
10	DA	C2	153.84
10	DA	C8	141.14
11	DG	C8	141.53
11	DG	N1	144.59
12	DG	C8	137.43
12	DG	N1	144.58
13	DG	C8	140.17
14	DT	C6	139.46
14	DT	C7	14.06
15	DT	C6	139.04
15	DT	C7	14.39
16	DA	C2	156.54
16	DA	C8	141.22
17	DG	C8	141.14
17	DG	N1	144.54
18	DG	C8	138.21
18	DG	N1	143.74

All atoms

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

Backbone atoms

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

Side chain atoms

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

Methyl group atoms

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

Aromatic group atoms

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

Histogram of normalized assigned chemical shifts

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Found 1 Document (0.319 seconds)

BMRB: 28081

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. Trimolecular G-quadruplex, : 1 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail