2M20

EGFR transmembrane - juxtamembrane (TM-JM) segment in bicelles: MD guided NMR refined structure.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
2	2D 1H-13C HSQC	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
3	3D HNCO	0.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
4	3D HNCA	0.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
5	3D HNCACB	0.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
6	3D HN(CO)CA	0.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
7	3D 1H-15N NOESY	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
8	3D 1H-13C NOESY	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
9	3D HCCH-COSY	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
10	3D HCCH-TOCSY	0.300 mM [U-100% 13C; U-100% 15N] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312
11	3D 15N-13C F1 filtered/F3 edited NOESY-HSQC	0.300 mM EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 18.8 mM [U-99% 2H] DMPC (D54), 77.86 mM [U-99% 2H] DHPC (D22), 0.300 mM EGFR TM-JM	90% H2O/10% D2O	0.05	6.2	ambient	312
12	2D 1H-15N TROSY	0.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] EGFR TM-JM, 50 mM MES, 5 mM TCEP, 1 mM EDTA, 0.05 mM AMESF, 10 % [U-2H] D2O, 0.02 % sodium azide, 9.4 mM [U-99% 2H] DMPC (D54), 37.98 mM [U-99% 2H] DHPC (D22)	90% H2O/10% D2O	0.05	6.2	ambient	312

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Avance-II	900
2	Bruker	Avance	800
3	Bruker	Avance	600

NMR Refinement
Method	Details	Software
simulated annealing	1. The TM-JM dimer structure was calculated with 38 interchain NOEs (19 interchain NOE restraint per monomer). There are too few interchain NOEs to determine the configuration of the TM-JM dimer unambiguously. Therefore, we used observations from molecular dynamics simulations of the TM-JM segment in DMPC lipid bilayers (see Arkhipov et al. 2013, Cell in press; companion paper to the paper describing the analysis of the TM-JM structure in an experimental context), and selected a initial structure of the TM-JM dimer with a dimeric conformation of right handed crossing angles that was stable during the MD simulations. It was then refined using NMR restraints. 2. The secondary structure analysis suggested that the juxtamembrane -A segment has a 30% probability of helix formation. In order to model the juxtamembrane dimer we assumed that the juxtamembrane-A segment only forms a dimer when both juxtamembrane segments are helical.	TOPSPIN

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	50
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TOPSPIN	v1.3	Bruker Biospin
2	processing	NMRDraw	v3.0	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	processing	NMRPipe	v3.0	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	chemical shift assignment	SPARKY	v3.114	Goddard
5	peak picking	SPARKY	v3.114	Goddard
6	data analysis	TALOS+		Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax,
7	structure solution	CNS	v1.3	Brunger, Adams, Clore, Gros, Nilges and Read
8	refinement	CNS	v1.3	Brunger, Adams, Clore, Gros, Nilges and Read
9	data analysis	ProcheckNMR		Laskowski and MacArthur
10	data analysis	PSVS		Bhattacharya and Montelione
11	data analysis	Molmol		Koradi, Billeter and Wuthrich

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.