BMRB: 50236

WT1-KTS RNA complex

Authors

Nishikawa, T., Wojciak, J.M., Dyson, H., Wright, P.E.

Assembly

WT1(-KTS) complex with RNA aptamer

Entity

1. WT1(-KTS) complex with RNA aptamer, entity 1 (polymer, Thiol state: all other bound), 117 monomers, 14290.22 Da Detail

EKRPFMCAYP GCNKRYFKLS HLQMHSRKHT GEKPYQCDFK DCERRFSRSD QLKRHQRRHT GVKPFQCKTC QRKFSRSDHL KTHTRTHTGE KPFSCRWPSC QKKFARSDEL VRHHNMH

2. WT1(-KTS) complex with RNA aptamer, entity 2 (polymer, Thiol state: not present), 29 monomers, 9361.565 Da Detail

GGGCCACCAA CGACAUUGAU AUGGUGCCC

3. WT1(-KTS) complex with RNA aptamer, entity ZN (non-polymer), 65.409 × 3 Da

Total weight

23848.012 Da

Max. entity weight

14290.22 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 80.1 %, Completeness: 29.8 %, Completeness (bb): 54.8 % Detail

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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	29.8 % (578 of 1940)	13.0 % (135 of 1042)	44.6 % (334 of 749)	73.2 % (109 of 149)
Backbone	54.8 % (553 of 1009)	28.1 % (114 of 406)	67.1 % (330 of 492)	98.2 % (109 of 111)
Sidechain	12.5 % (131 of 1044)	3.3 % (21 of 636)	29.7 % (110 of 370)	0.0 % (0 of 38)
Aromatic	0.0 % (0 of 286)	0.0 % (0 of 143)	0.0 % (0 of 129)	0.0 % (0 of 14)
Methyl	4.3 % (2 of 46)	0.0 % (0 of 23)	8.7 % (2 of 23)

1. entity 1

EKRPFMCAYP GCNKRYFKLS HLQMHSRKHT GEKPYQCDFK DCERRFSRSD QLKRHQRRHT GVKPFQCKTC QRKFSRSDHL KTHTRTHTGE KPFSCRWPSC QKKFARSDEL VRHHNMH

2. entity 2

GGGCCACCAA CGACAUUGAU AUGGUGCCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled protein, unlabeled RNA

#	Name	Isotope labeling	Type	Concentration
1	WT1(-KTS)	[U-100% 13C; U-100% 15N; U-90% 2H]		0.55 (±0.1) mM
2	aptamer RNA	natural abundance		0.55 (±0.1) mM
3	TRIS	[U-100% 2H]		10 (±0.1) mM
4	potassium chloride	natural abundance		350 (±0.5) mM
5	DTT	natural abundance		10 (±0.1) mM
6	ZnSO4	natural abundance		5 (±0.1) uM
7	sodium azide	natural abundance		2 (±0.1) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled protein, unlabeled RNA

#	Name	Isotope labeling	Type	Concentration
8	WT1(-KTS)	[U-100% 13C; U-100% 15N; U-65% 2H]		0.55 (±0.1) mM
9	aptamer RNA	natural abundance		0.55 (±0.1) mM
10	TRIS	[U-100% 2H]		10 (±0.1) mM
11	potassium chloride	natural abundance		350 (±0.5) mM
12	DTT	natural abundance		10 (±0.1) mM
13	ZnSO4	natural abundance		5 (±0.1) uM
14	sodium azide	natural abundance		2 (±0.1) mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled RNA, unlabeled protein

#	Name	Isotope labeling	Type	Concentration
15	WT1(-KTS)	natural abundance		0.55 (±0.1) mM
16	aptamer RNA	[U-99% 13C; U-99% 15N]		0.55 (±0.1) mM
17	TRIS	[U-100% 2H]		10 (±0.1) mM
18	potassium chloride	natural abundance		350 (±0.5) mM
19	DTT	natural abundance		10 (±0.1) mM
20	ZnSO4	natural abundance		5 (±0.1) uM
21	sodium azide	natural abundance		2 (±0.1) mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled RNA, unlabeled protein

#	Name	Isotope labeling	Type	Concentration
22	WT1(-KTS)	natural abundance		0.55 (±0.1) mM
23	aptamer RNA	[U-100% 15N]		0.55 (±0.1) mM
24	TRIS	[U-100% 2H]		10 (±0.1) mM
25	potassium chloride	natural abundance		350 (±0.5) mM
26	DTT	natural abundance		10 (±0.1) mM
27	ZnSO4	natural abundance		5 (±0.1) uM
28	sodium azide	natural abundance		2 (±0.1) mM

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Chem. Shift Complete2

Sequence coverage: 28.1 %, Completeness: 24.2 %, Completeness (bb): 39.7 % Detail

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• BMRB/XML (partial)
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Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	24.2 % (940 of 3880)	15.1 % (314 of 2084)	33.9 % (508 of 1498)	39.6 % (118 of 298)
Backbone	39.7 % (801 of 2018)	28.6 % (232 of 812)	45.8 % (451 of 984)	53.2 % (118 of 222)
Sidechain	12.2 % (255 of 2088)	6.4 % (82 of 1272)	23.4 % (173 of 740)	0.0 % (0 of 76)
Aromatic	17.1 % (98 of 572)	17.5 % (50 of 286)	18.6 % (48 of 258)	0.0 % (0 of 28)
Methyl	6.5 % (6 of 92)	4.3 % (2 of 46)	8.7 % (4 of 46)

1. entity 1

EKRPFMCAYP GCNKRYFKLS HLQMHSRKHT GEKPYQCDFK DCERRFSRSD QLKRHQRRHT GVKPFQCKTC QRKFSRSDHL KTHTRTHTGE KPFSCRWPSC QKKFARSDEL VRHHNMH

2. entity 2

GGGCCACCAA CGACAUUGAU AUGGUGCCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled protein, unlabeled RNA

#	Name	Isotope labeling	Type	Concentration
1	WT1(-KTS)	[U-100% 13C; U-100% 15N; U-90% 2H]		0.55 (±0.1) mM
2	aptamer RNA	natural abundance		0.55 (±0.1) mM
3	TRIS	[U-100% 2H]		10 (±0.1) mM
4	potassium chloride	natural abundance		350 (±0.5) mM
5	DTT	natural abundance		10 (±0.1) mM
6	ZnSO4	natural abundance		5 (±0.1) uM
7	sodium azide	natural abundance		2 (±0.1) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled protein, unlabeled RNA

#	Name	Isotope labeling	Type	Concentration
8	WT1(-KTS)	[U-100% 13C; U-100% 15N; U-65% 2H]		0.55 (±0.1) mM
9	aptamer RNA	natural abundance		0.55 (±0.1) mM
10	TRIS	[U-100% 2H]		10 (±0.1) mM
11	potassium chloride	natural abundance		350 (±0.5) mM
12	DTT	natural abundance		10 (±0.1) mM
13	ZnSO4	natural abundance		5 (±0.1) uM
14	sodium azide	natural abundance		2 (±0.1) mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled RNA, unlabeled protein

#	Name	Isotope labeling	Type	Concentration
15	WT1(-KTS)	natural abundance		0.55 (±0.1) mM
16	aptamer RNA	[U-99% 13C; U-99% 15N]		0.55 (±0.1) mM
17	TRIS	[U-100% 2H]		10 (±0.1) mM
18	potassium chloride	natural abundance		350 (±0.5) mM
19	DTT	natural abundance		10 (±0.1) mM
20	ZnSO4	natural abundance		5 (±0.1) uM
21	sodium azide	natural abundance		2 (±0.1) mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.1, Details protein-RNA complex; labeled RNA, unlabeled protein

#	Name	Isotope labeling	Type	Concentration
22	WT1(-KTS)	natural abundance		0.55 (±0.1) mM
23	aptamer RNA	[U-100% 15N]		0.55 (±0.1) mM
24	TRIS	[U-100% 2H]		10 (±0.1) mM
25	potassium chloride	natural abundance		350 (±0.5) mM
26	DTT	natural abundance		10 (±0.1) mM
27	ZnSO4	natural abundance		5 (±0.1) uM
28	sodium azide	natural abundance		2 (±0.1) mM

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Release date

2020-04-13

Citation

RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1
Nishikawa, T., Wojciak, J.M., Dyson, H., Wright, P.E.
Biochemistry (2020), 59, 3889-3901, PubMed 32955251 , DOI 10.1021/acs.biochem.0c00602 , Abstract

Related entities 1. WT1(-KTS) complex with RNA aptamer, entity 1, : 1 : 4 : 1 : 4 : 458 entities Detail

Related entities 2. WT1(-KTS) complex with RNA aptamer, entity 2, : 1 entities Detail

Interaction partners 1. WT1(-KTS) complex with RNA aptamer, entity 1, : 14 interactors Detail

Experiments performed 20 experiments Detail

Chemical shift validation 6 contents Detail