BMRBj - BMREntryMaster

Found 1 Document (0.317 seconds)

BMRB: 34542

Antiparallel basket-type G-quadruplex DNA structure formed in human Bcl-2 promoter containing 8-oxoG

Authors

Bielskute, S., Plavec, J., Podbevsek, P.

Assembly

bcl2ex-oxoG19

Entity

1. bcl2ex-oxoG19 (polymer, Thiol state: not present), 25 monomers, 8040.066 Da Detail

CGGGCGCGGG AGGAAGGGXG CGGGA

Formula weight

8040.066 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 63.8 %, Completeness (bb): 55.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	63.8 % (143 of 224)	63.8 % (143 of 224)
Suger, PO4	55.4 % (93 of 168)	55.4 % (93 of 168)
Nucleobase	89.3 % (50 of 56)	89.3 % (50 of 56)
Aromatic	95.8 % (46 of 48)	95.8 % (46 of 48)

1. entity 1

CGGGCGCGGG AGGAAGGGXG CGGGA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 298 K, pH 7, Details 1.2 mM NA bcl2ex-oxoG19, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	bcl2ex-oxoG19	natural abundance		1.2 mM

Sample #2

Solvent system 100% D2O, Pressure 101325 Pa, Temperature 298 K, pH 7, Details 1.2 mM NA bcl2ex-oxoG19, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	bcl2ex-oxoG19	natural abundance		1.2 mM

Release date

2020-08-23

Citation

Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter
Bielskute, S., Plavec, J., Podbevsek, P.
Nucleic Acids Res. (2021), 49, 2346-2356, PubMed 33638996 , DOI 10.1093/nar/gkab057 , Abstract

Experiments performed 4 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34542_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	19	8OG	8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts

Content subtype: bmr34542_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	180		100.0 (chain: 1, length: 25)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 25, Sequence coverage: 100.0%

--------10--------20-----
CGGGCGCGGGAGGAAGGGXGCGGGA
|||||||||||||||||||||||||
CGGGCGCGGGAGGAAGGGXGCGGGA

Total number of assignments
- ¹H chemical shifts: 152
- ¹³C chemical shifts: 28

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
19	8OG

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DC	C6	143.57
2	DG	C8	142.11
3	DG	C8	138.97
4	DG	C8	142.78
5	DC	C6	144.33
6	DG	H21	5.7
6	DG	H22	5.8
6	DG	C8	138.62
7	DC	C6	144.57
8	DG	C8	137.84
9	DG	C8	141.26
10	DG	C8	136.73
11	DA	C2	156.79
11	DA	C8	140.56
12	DG	C8	137.69
13	DG	C8	138.89
14	DA	C2	155.48
14	DA	C8	140.55
15	DA	C2	155.62
15	DA	C8	140.05
16	DG	C8	142.11
17	DG	C8	137.43
18	DG	C8	140.34
20	DG	C8	138.25
21	DC	C6	148.81
22	DG	C8	137.09
23	DG	C8	140.91
24	DG	C8	136.13
25	DA	C2	155.75
25	DA	C8	142.6

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	224	143	63.8

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	93	55.4

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	50	89.3

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	24	24	100.0

Histogram of normalized assigned chemical shifts

Keywords 8-oxo-Guanine, DNA, G-quadruplex, bcl2, oxidative stress, promoter

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Found 1 Document (0.317 seconds)

BMRB: 34542

Sample #1

Sample #2

Experiments performed 4 experiments Detail

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Sample

Instrument

Sample

Instrument

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Chemical shift validation 3 contents Detail