6SDW | pdb_00006sdw

Solution structure of Staufen1 dsRBD3+4 - hARF1 SBS dsRNA complex.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
2	2D 1H-15N HSQC	310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
3	2D 1H-15N HSQC	310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 950
4	2D 1H-13C HSQC aliphatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
5	2D 1H-13C HSQC aliphatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
6	3D HNCA	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
7	3D HNCO	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
8	3D CBCA(CO)NH	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
9	3D HNCACB	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
10	3D HBHA(CO)NH	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
11	3D HcccoNH-TOCSY	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
12	3D CccoNH-TOCSY	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
13	3D 1H-13C NOESY aliphatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
14	3D 1H-13C NOESY aromatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
15	3D 1H-15N NOESY	310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 950
16	2D 1H-1H, 13C 2F-filtered NOESY	451 uM [U-13C; U-15N] Staufen1 dsRDB4, 451 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
17	3D 13C 1F-filtered 2F-edited HSQC-NOESY	451 uM [U-13C; U-15N] Staufen1 dsRDB4, 451 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
18	3D 1H-13C NOESY ribose	354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
19	2D 1H-1H TOCSY	310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
20	2D 1H-1H NOESY	310 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
21	2D 1H-13C HSQC	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
22	3D HCCH-TOCSY	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
23	3D 1H-13C NOESY	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
24	2D 1H-13C HSQC aliphatic	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
25	2D 13C 1F-filtered 2F-filtered NOESY	451 uM [U-13C; U-15N] Staufen1 dsRDB4, 451 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
26	2D 1H-13C HSQC	354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
27	2D 1H-1H TOCSY	310 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
28	2D 1H-1H NOESY	310 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
29	3D HCCH-COSY aromatic	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
30	2D 1H-15N HSQC	417 uM [U-15N] Staufen1 dsRBD3, 417 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
31	2D 1H-15N HSQC	417 uM [U-15N] Staufen1 dsRBD3, 417 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
32	2D 1H-15N HSQC	417 uM [U-15N] Staufen1 dsRBD3, 417 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 950
33	2D 1H-13C HSQC aliphatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
34	2D 1H-13C HSQC aliphatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
35	3D HNCA	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
36	3D HNCO	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
37	3D CBCA(CO)NH	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
38	3D HNCACB	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
39	3D HBHA(CO)NH	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
40	3D HA(CO)NH	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
41	3D HcccoNH-TOCSY	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
42	3D CccoNH-TOCSY	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
43	3D HCCH-TOCSY	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
44	3D HCCH-TOCSY	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
45	3D 1H-13C NOESY aliphatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
46	3D 1H-13C NOESY aromatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
47	2D 1H-13C HSQC aliphatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
48	2D 1H-13C HSQC aromatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
49	2D 1H-13C HSQC aromatic	458 uM [U-13C; U-15N] Staufen1 dsRBD3, 458 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
50	3D 1H-15N NOESY	417 uM [U-15N] Staufen1 dsRBD3, 417 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 950
51	2D 1H-1H, 13C 2F-filtered NOESY	157 uM [U-13C; U-15N] Staufen1 dsRBD3, 157 uM Unlabelled Staufen1 dsRBD4, 157 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
52	2D 1H-1H, 13C 1F-filtered 2F-filtered NOESY	157 uM [U-13C; U-15N] Staufen1 dsRBD3, 157 uM Unlabelled Staufen1 dsRBD4, 157 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
53	3D 13C 1F-filtered 2F-edited HSQC-NOESY	157 uM [U-13C; U-15N] Staufen1 dsRBD3, 157 uM Unlabelled Staufen1 dsRBD4, 157 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
54	2D 1H-13C HSQC aromatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 700
55	2D 1H-13C HSQC aromatic	405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1	90-95% H2O/5-10% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
56	2D 1H-13C HSQC aliphatic	451 uM [U-13C; U-15N] Staufen1 dsRDB4, 451 uM Unlabelled hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
57	2D 1H-13C HSQC aromatic	478 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
58	2D 1H-13C HSQC ribose	354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850
59	2D 1H-13C HSQC aromatic	354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1	100% D2O	50 mM	6.5	ambient atm	308	Bruker AVANCE III 850

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	700
2	Bruker	AVANCE III	850
3	Bruker	AVANCE III	950

NMR Refinement
Method	Details	Software
simulated annealing		Amber
na		PROCHECK / PROCHECK-NMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy and restraint violation
Conformers Calculated Total Number	50
Conformers Submitted Total Number	20
Representative Model	1 (medoid)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	AMBER14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	CYANA	cyana-3.98.5	Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	CARA	cara_1.8.4	Keller, Damberger and Wuthrich
4	peak picking	CARA	cara_1.8.4	Keller, Damberger and Wuthrich
5	chemical shift assignment	Sparky	SPARKY3	Goddard and Kneller
6	structure calculation	ATNOS-CANDID	UNIO 2.0.3	Herrmann and Guntert
7	peak picking	Sparky	SPARKY3	Goddard and Kneller
8	collection	TopSpin	TOPSPIN3.2	Bruker Biospin
9	processing	TopSpin	TOPSPIN3.2	Bruker Biospin
10	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
11	refinement	PROCHECK / PROCHECK-NMR		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton