2L29 | pdb_00002l29

Complex structure of E4 mutant human IGF2R domain 11 bound to IGF-II

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D 1H-13C NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
2	3D 1H-15N NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
3	3D 1H-15N NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
4	3D 1H-13C NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
5	2D 1H-15N HSQC	0.5-1 mM [U-98% 15N; U-95% 2H] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
6	3D 1H-15N NOESY	0.5-1 mM [U-98% 15N; U-95% 2H] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
7	2D 1H-15N HSQC	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
8	2D 1H-13C HSQC	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
9	3D HNCO	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
10	3D CBCA(CO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
11	3D C(CO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
12	3D HNCA	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
13	3D HNCACB	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
14	3D HNCACB	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
15	3D HCCH-TOCSY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
16	3D HN(CO)CA	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
17	3D H(CCO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
18	3D 1H-15N NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
19	3D 1H-13C NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
20	2D 1H-15N HSQC	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
21	2D 1H-13C HSQC	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
22	3D CBCA(CO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
23	3D C(CO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
24	3D HNCO	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
25	3D HNCA	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
26	3D HNCACB	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
27	3D HN(CO)CA	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
28	3D H(CCO)NH	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
29	3D HCCH-TOCSY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
30	3D 1H-15N NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
31	3D 1H-13C NOESY	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
32	2D f2 filter noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
33	2D f2 filter noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
34	2D f2 filter noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
35	2D f2 filter noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
36	2D CN filtered noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
37	2D CN filtered noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
38	2D CN filtered noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
39	2D CN filtered noesy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
40	2D CN filtered tocsy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 1.-1.5 mM IGF2, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310
41	2D CN filtered tocsy	0.5-1 mM [U-98% 13C; U-98% 15N] IGF2, 1.-1.5 mM IGF2R, 5 % D2O, 100 uM sodium azide, 5 mM sodium acetate, 0.1 mM EDTA	95% H2O/5% D2O	0	4.2	ambient	310

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	VNMRS	600
3	Varian	UNITYPLUS	900

NMR Refinement
Method	Details	Software
simulated annealing, simulated annealing	ARIA2.2 protocol. Cool_1 and cool_2 steps increased to 40K and cool_2, ARIA2.2 water refinement modified with RECOORD water refinement parameters	VnmrJ

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VnmrJ		Varian
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
4	refinement	iCing	r765	Vuister, Doreleijers, Sousa da Silva
5	chemical shift assignment	Analysis	2.13	CCPN
6	data analysis	Analysis	2.13	CCPN
7	refinement	ARIA	2.2	Linge, O'Donoghue and Nilges
8	structure solution	ARIA	2.2	Linge, O'Donoghue and Nilges
9	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
10	structure solution	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read