2K3U

Structure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.

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	0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
2	2D 1H-15N HSQC	0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
3	2D 1H-15N HSQC	0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
4	2D 1H-13C HSQC	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
5	2D 1H-13C HSQC	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
6	2D 1H-13C HSQC	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
7	3D CBCA(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
8	3D HNCACB	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
9	3D HNCO	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
10	3D HBHACBCA(CO)NH	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
11	3D HCCH-TOCSY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
12	3D HCCH-TOCSY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
13	3D 1H-15N NOESY	0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
14	3D 1H-15N NOESY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
15	3D 1H-15N TOCSY	0.5 mM [U-99% 15N] protein, 0.5 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
16	3D 1H-13C NOESY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
17	3D 1H-13C NOESY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
18	2D 1H-1H NOESY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
19	2D 1H-1H TOCSY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
20	3D COCA(HN)	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
21	3D-CNH-NOESY	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
22	2D-HBHD aromatic	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
23	2D-HBHE aromatic	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
24	2D-CBHD aromatic	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
25	2D-CBHE aromatic	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
26	3D HNHA	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298
27	3D HNHB	1.0 mM [U-99% 13C; U-99% 15N] protein, 1.0 mM entity_2, 20 mM sodium phosphate, 0.1 % sodium azide, 90 % H2O, 10 % D2O	90% H2O/10% D2O	20	6.5	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	500
3	Bruker	AVANCE	900

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics, simulated annealing docking, molecular dynamics	THE ARIA1.2 / CNS1.1 SIMULATED ANNEALING PROTOCOL HAS BEEN APPLIED TO SOLVE THE NMR STRUCTURE SEPARATELY FOR BOTH THE CHIPS PROTEIN AND THE C5AR(P7-28S) PEPTIDE, WHEN BOUND IN THE COMPLEX. 160 STRUCTURES OF CHIPS AND P7-28S PEPTIDE (IN ITS DESULFATED STATE) WERE CALCULATED EACH. THE 60 LOWEST-ENERGY ARIA STRUCTURES WERE INITIALLY SELECTED FOR THE PROTEIN. COORDINATES OF THE 60 PROTEIN STRUCTURES ARE SUBSEQENTLY AVERAGED OVER THE ENSEMBLE (BACKBONE RMSD RESIDUE 36-113 = 0.275 ANGSTROM), WITH SIDECHAINS REGULARLIZED BY SIMULATED ANNEALING ENERGY- MINIMIZATION. THIS AVERAGE STRUCTURE IS USED AS REFERENCE FOR SUBSEQUENT DOCKING WITH THE THREE LOWEST ENERGY CONFORMERS OF THE P7-28 PEPTIDE. THE THREE LOW-ENERGY PEPTIDE STRUCTURES WERE TAKEN DIRECTLY FROM THE ARIA GENERATED ENSEMBLE CALCULATED BASED ON PEPTIDE-PEPTIDE NOES FROM THE 900 MHZ [15N,13C]-FILTERED 2D NOESY. DISTANCE RESTRAINT MD-DOCKING BETWEEN THE EXPERIMENTALLY DERIVED ARIA1.2 STRUCTURE OF THE (SULPHATE PATCHED) PEPTIDE AND THE AVERAGE CHIPS PROTEIN STRUCTURE WAS PERFORMED USING THE YASARA STRUCTURE/WHATIF 8.3.3 TWINSET SOFTWARE. DOCKING WAS DRIVEN BY A LARGE NUMBER OF INTERMOLECULAR NOES BETWEEN PROTEIN AND PEPTIDE, DERIVED FROM VARIOUS ISOTOPE-FILTERED 2D- AND 3D-NMR EXPERIMENTS RUN ON THE COMPLEX. 25 FINAL STRUCTURES WERE SELECTED, BASED ON THE CRITERIA OF A COMBINATION OF LOW RESTRAINT VIOLATION ENERGY AND BEST PREDICTED BACK-CALCULATED PROTON CHEMICAL SHIFTS AT THE PEPTIDE-PROTEIN BINDING INTERFACE. THE SELECTED STRUCTURES WERE REFINED IN EXPLICIT SOLVENT. STEREOSPECIFIC ASSIGNMENTS AND FLOATING ASSIGNMENTS ARE INDICATED IN THE B-FACTOR COLUMN OF THE PDB COORDINATES. A VALUE OF 50 MEANS A FLOATING ASSIGNMENT HAS BEEN APPLIED TO THIS PROTON PAIR. A VALUE OF 75 INDICATES A STEREOSPECIFIC ASSIGNMENT OF METHYL AND METHYLENE PROTON PAIRS IN THE CORRESPONDING STRUCTURE MODEL.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	130
Conformers Submitted Total Number	25
Representative Model	1 (lowest energy and chemical shift difference)

Additional NMR Experimental Information

Details

STANDARD TRIPLE RESONANCE EXPERIMENTS WERE USED FOR ASSIGNMENT AND STRUCTURE DETERMINATION OF THE CHIPS PROTEIN. THE UNLABELLED PEPTIDE C5AR(P7-28S) IN THE COMPLEX HAS BEEN SOLVED BY MEANS OF ISOTOPE-FILTERED 2D SPECTRA. TO EXTRACT INTERMOLECULAR NOE'S BETWEEN [15N,13C] LABELLED CHIPS PROTEIN AND UNLABELLED C5AR(P7-28S) PEPTIDE, SEVERAL 2D-13C-FILTERED NOESY AND 3D 13C-EDITED-13C-FILTERED NOESY SPECTRA WERE RECORDED AT 900 MHZ. FOR THE 3D FILTERED SPECTRA THE 13C-HSQC DETECTION STEP WAS OPTIMIZED BY RECORDING TWO SPECTRA, ONE WITH THE 13C CARRIER FREQUENCY PLACED IN THE AROMATIC REGION, AND ONE WITH THE 13C CARRIER FREQUENCY SET TO THE ALIFATIC REGION. THE MIXING TIME USED WAS 200 MS, TO FORCE A GOOD SENSITIVITY NECESSARY FOR THE COLLECTION OF A SUFFICIENT NUMBER OF INTERMOLECULAR NOE'S.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	3.5	Bruker Biospin
2	processing	XwinNMR	3.5	Bruker Biospin
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	refinement	ARIA	1.2	Linge, O'Donoghue and Nilges
6	structure solution	ARIA	1.2	Linge, O'Donoghue and Nilges
7	structure solution	CNSSOLVE	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
8	peak picking	Sparky	3.112	Goddard
9	chemical shift assignment	Sparky	3.112	Goddard
10	peak picking	CARA	1.3.2	Keller and Wuthrich
11	chemical shift assignment	CARA	1.3.2	Keller and Wuthrich
12	collection	VNMR		Varian
13	data analysis	MOLMOL		Koradi, Billeter and Wuthrich
14	data analysis	ProcheckNMR		Laskowski and MacArthur
15	structure solution	TALOS		Cornilescu, Delaglio and Bax
16	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
17	structure solution	YASARA	Yasara Structure 8.3.3/WHATIF	Krieger and Vriend
18	refinement	YASARA	Yasara Structure 8.3.3/WHATIF	Krieger and Vriend
19	chemical shift calculation	SHIFTCALC	2004	Williamson and Refaee
20	chemical shift assignment	PACES		(PACES) Coggins and Zhou