2K3U
Structure of the tyrosine-sulfated C5a receptor N-terminus in complex with the immune evasion protein CHIPS.
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 500 |
3 | Bruker | AVANCE | 900 |
NMR Refinement | ||
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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 | |
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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 | |
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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 | ||||
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# | 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 |