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Found 1 Document (0.341 seconds)

BMRB: 34312

Solution structure of the RNA duplex formed by the 5'-end of U1snRNA and the 5'-splice site of SMN2 exon7 in complex with the SMN-C5 splicing modifier

Authors

Campagne, S., Allain, F.H.

Assembly

RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'), RNA (5'-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3')

Entity

1. RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'), RNA (5'-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'), entity 1 (polymer, Thiol state: not present), 11 monomers, 3491.046 Da Detail

AUACXXACCU G

2. RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'), RNA (5'-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'), entity 2 (polymer, Thiol state: not present), 11 monomers, 3610.134 Da Detail

GGAGUAAGUC U

3. RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'), RNA (5'-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'), entity GDZ (non-polymer), 392.429 Da

Total weight

7493.609 Da

Max. entity weight

3610.134 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.9 %, Completeness: 94.8 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C
All	94.8 % (292 of 308)	90.8 % (157 of 173)	100.0 % (135 of 135)
Suger, PO4	100.0 % (220 of 220)	100.0 % (120 of 120)	100.0 % (100 of 100)
Nucleobase	81.8 % (72 of 88)	69.8 % (37 of 53)	100.0 % (35 of 35)
Aromatic	90.0 % (72 of 80)	82.2 % (37 of 45)	100.0 % (35 of 35)

1. entity 1

AUACXXACCU G

2. entity 2

GGAGUAAGUC U

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5, Details 10 mM deuterated MES, 50 mM unlabelled sodium chloride, 6 % deuterated glycerol, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.8 mM
2	entity_2	natural abundance	0.8 mM
3	entity_3	natural abundance	1.6 mM
4	MES	[U-2H]	10 mM
5	sodium chloride	natural abundance	50 mM
6	glycerol	[U-2H]	6 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5, Details 10 mM deuterated MES, 50 mM unlabled sodium chloride, 6 % deuterated glycerol, 100% D2O

#	Name	Isotope labeling	Concentration
7	entity_1	natural abundance	0.8 mM
8	entity_2	natural abundance	0.8 mM
9	entity_3	natural abundance	1.6 mM
10	MES	[U-2H]	10 mM
11	sodium chloride	natural abundance	50 mM
12	glycerol	[U-2H]	6 %

Release date

2019-08-05

Citation

Structural basis of a small molecule targeting RNA for a specific splicing correction
Campagne, S., Boigner, S., Rudisser, S., Moursy, A., Gillioz, L., Knorlein, A., Hall, J., Ratni, H., Clery, A., Allain, F.H.
Nat. Chem. Biol. (2019), 15, 1191-1198, PubMed 31636429 , DOI 10.1038/s41589-019-0384-5 , Abstract

Experiments performed 5 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker 900 Avance - 900 MHz cryo probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5, Details 10 mM deuterated MES, 50 mM unlabelled sodium chloride, 6 % deuterated glycerol, 100% D2O

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.8 mM
2	entity_2	natural abundance	0.8 mM
3	entity_3	natural abundance	1.6 mM
4	MES	[U-2H]	10 mM
5	sodium chloride	natural abundance	50 mM
6	glycerol	[U-2H]	6 %

2 2D 1H-1H NOESY

Instrument

Bruker 900 Avance - 900 MHz cryo probe

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.8 mM
2	entity_2	natural abundance	0.8 mM
3	entity_3	natural abundance	1.6 mM
4	MES	[U-2H]	10 mM
5	sodium chloride	natural abundance	50 mM
6	glycerol	[U-2H]	6 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker 900 Avance - 900 MHz cryo probe

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.8 mM
2	entity_2	natural abundance	0.8 mM
3	entity_3	natural abundance	1.6 mM
4	MES	[U-2H]	10 mM
5	sodium chloride	natural abundance	50 mM
6	glycerol	[U-2H]	6 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker 900 Avance - 900 MHz cryo probe

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.8 mM
2	entity_2	natural abundance	0.8 mM
3	entity_3	natural abundance	1.6 mM
4	MES	[U-2H]	10 mM
5	sodium chloride	natural abundance	50 mM
6	glycerol	[U-2H]	6 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker 600 Avance - 600 MHz cryo probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 5.5, Details 10 mM deuterated MES, 50 mM unlabled sodium chloride, 6 % deuterated glycerol, 100% D2O

#	Name	Isotope labeling	Concentration
7	entity_1	natural abundance	0.8 mM
8	entity_2	natural abundance	0.8 mM
9	entity_3	natural abundance	1.6 mM
10	MES	[U-2H]	10 mM
11	sodium chloride	natural abundance	50 mM
12	glycerol	[U-2H]	6 %

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34312_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	5	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts
1	6	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts
3	1	GDZ	2-(8-fluoranyl-2-methyl-imidazo[1,2-a]pyridin-6-yl)-7-(4-methylpiperazin-1-yl)pyrido[1,2-a]pyrimidin-4-one	Assigned chemical shifts

Content subtype: bmr34312_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	341		100.0 (chain: 1, length: 11), 100.0 (chain: 2, length: 11), 100.0 (chain: 3, length: 1)
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: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: 3, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 194
  - ¹³C chemical shifts: 147
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 3
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	87	83.7
¹³C chemical shifts	80	74	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	66	97.1
¹³C chemical shifts	55	55	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	21	58.3
¹³C chemical shifts	25	19	76.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	7	100.0
¹³C chemical shifts	7	7	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	93	86	92.5
¹³C chemical shifts	73	73	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	66	100.0
¹³C chemical shifts	55	55	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	20	74.1
¹³C chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0
¹³C chemical shifts	10	10	100.0

Comp_index_ID	Comp_ID
1	GDZ

Keywords 5'-splice site bulge repair, RNA, Spinal Muscular Atrophy, U1 snRNA, bulge nucleotide, splicing modifier

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Found 1 Document (0.341 seconds)

BMRB: 34312

Sample #1

Sample #2

Experiments performed 5 experiments Detail

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Chemical shift validation 5 contents Detail