8DGK | pdb_00008dgk

NMR structure of calmodulin bound to N-terminal site in the beta-subunit of cyclic nucleotide-gated channel

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
2	3D HNCO	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
3	3D HNCA	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
4	3D HNCACB	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
5	3D CBCA(CO)NH	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
15	3D HBHA(CO)NH	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
14	3D HBHANH	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
13	3D C(CO)NH	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
12	3D H(CCO)NH	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	90% H2O/10% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
11	2D 1H-13C HSQC	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
10	2D 1H-13C HSQC	0.5 mM [U-10% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
9	3D HCCH-TOCSY	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
8	3D 1H-13C NOESY	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
7	2D 1H-13C HSQC aromatic	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800
6	2D 1H-1H NOESY	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 600
16	2D 1H-1H NOESY	0.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride	100% D2O	1 mM	7	1 atm	308	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600
2	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing	The authors state that for the structure of the calmodulin N-lobe, they used residues 4-81 from the available structure of the calmodulin/IQ domain complex (PDB ID - 2F3Y, chain A). The structure of the peptide fragment of the Cyclic nucleotide-gated cation channel beta-1 was generated in Modeller 9.25 using the template of the peptide of cyclic-nucleotide-gated olfactory channel (PDB ID - 1SY9, chain B). Finally, the HADDOCK calculation was performed on an energy minimized peptide obtained after energy minimization in Gromacs.	HADDOCK

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	HADDOCK		Bonvin
2	structure calculation	HADDOCK		Bonvin
3	chemical shift assignment	Sparky		Goddard
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.