BMRBj - BMREntryMaster

Found 1 Document (0.315 seconds)

BMRB: 30622

6PK9

Solution Structure of lncRNA (LINK-A) 20-nt Hexaloop Hairpin

Authors

Amado, A.Y., Walker, M., Varani, G.

Assembly

LINK-A

Entity

1. LINK-A (polymer, Thiol state: not present), 20 monomers, 6477.826 Da Detail

GGAGGGUAGA CUCGCUCUCC

Formula weight

6477.826 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.8 %, Completeness (bb): 72.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	77.8 % (249 of 320)	75.0 % (132 of 176)	82.0 % (109 of 133)	72.7 % (8 of 11)
Suger, PO4	72.7 % (160 of 220)	70.0 % (84 of 120)	76.0 % (76 of 100)
Nucleobase	89.0 % (89 of 100)	85.7 % (48 of 56)	100.0 % (33 of 33)	72.7 % (8 of 11)
Aromatic	94.3 % (83 of 88)	95.5 % (42 of 44)	100.0 % (33 of 33)	72.7 % (8 of 11)

1. entity 1

GGAGGGUAGA CUCGCUCUCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0, Details 0.9 mM RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	RNA	natural abundance	0.9 mM
2	Sodium Phosphate	natural abundance	20 mM
3	EDTA	natural abundance	0.01 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0, Details 0.6 mM RNA, 100% D2O

#	Name	Isotope labeling	Concentration
4	RNA	natural abundance	0.6 mM
5	Sodium Phosphate	natural abundance	20 mM
6	EDTA	natural abundance	0.01 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0, Details 0.5 mM [U-13C; U-15N] RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	RNA	[U-13C; U-15N]	0.5 mM
8	Sodium Phosphate	natural abundance	20 mM
9	EDTA	natural abundance	0.01 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0, Details 0.5 mM [U-13C; U-15N] RNA, 100% D2O

#	Name	Isotope labeling	Concentration
10	RNA	[U-13C; U-15N]	0.5 mM
11	Sodium Phosphate	natural abundance	20 mM
12	EDTA	natural abundance	0.01 mM

Release date

2019-08-01

Citation

Structure of the lncRNA LINK-A Hexaloop Hairpin in PI(3,4,5)P3 Interaction
Amado, A.Y., Walker, M., Varani, G.

Related entities 1. LINK-A, : 1 entities Detail

Experiments performed 6 experiments Detail

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30622_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: bmr30622_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	280		100.0 (chain: 1, length: 20)
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: 20, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 163
- ¹³C chemical shifts: 109
- ¹⁵N chemical shifts: 8

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	HO2'	4.907
2	G	H22	5.685
2	G	HO2'	4.643
3	A	H61	7.945
3	A	H62	6.747
3	A	HO2'	4.641
4	G	H21	7.848
4	G	H22	5.765
4	G	HO2'	4.456
5	G	H21	6.111
5	G	H22	5.515
5	G	HO2'	4.732
6	G	H21	8.463
6	G	H22	6.323
6	G	HO2'	4.545
7	U	HO2'	4.256
8	A	HO2'	4.471
9	G	HO2'	4.546
10	A	HO2'	4.656
11	C	HO2'	4.197
12	U	HO2'	4.379
13	C	HO2'	4.439
14	G	H21	6.03
14	G	H22	5.522
14	G	HO2'	4.664
15	C	HO2'	4.472
16	U	HO2'	4.144
17	C	HO2'	3.946
18	U	HO2'	4.161
19	C	HO2'	4.31
20	C	HO2'	4.471

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	132	75.0
¹³C chemical shifts	133	109	82.0
¹⁵N chemical shifts	11	8	72.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	120	84	70.0
¹³C chemical shifts	100	76	76.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	48	85.7
¹³C chemical shifts	33	33	100.0
¹⁵N chemical shifts	11	8	72.7

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	13	13	100.0
¹³C chemical shifts	13	13	100.0

Histogram of normalized assigned chemical shifts

Keywords LINK-A, REPLICATION, RNA, hairpin, lncRNA

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Found 1 Document (0.315 seconds)

BMRB: 30622

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. LINK-A, : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail