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Materials and Methods: SPG7 (2QZ4)

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Structure	SPG7
PDB Code	2QZ4
Entry clone accession	gi\|62020635
Entry clone source	Mammalian Gene Collection
Tag	N-terminal hexahistidine tag with integrated TEV protease cleavage site: mhhhhhhssgvdlgtenlyfq*sm
Construct sequence	mhhhhhhssgvdlgtenlyfq*smGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYI DEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAR EGHTSVHTLNFEYAVERVLAGTAKKSKILSK
Vector	pNIC-Bsa4
Expression host	E.coli BL21-Gold(DE3)pRARE2, where BL21-Gold(DE3) cells (Stratagene) have been transformed with pRARE2 originating from the Rosetta2 strain (Novagen). The pRARE2 plasmid supplies tRNAs for rare codons.
Growth method	Freshly transformed cells were used to inoculate 40 mL TB supplemented with 8 g/l glycerol, 100 µg/mL kanamycin and 34 µg/mL chloramphenicol at 37 ºC overnight. The overnight culture (40 mL) was used to inoculate 2 x 1.5 l TB supplemented with 8 g/l glycerol, 50 µg/mL kanamycin, 34 µg/mL chloramphenicol and approximately 500 µl BREOX FMT 30 anti-foam solution (Cognis Performance Chemicals UK Ltd). The culture was grown in a LEX bioreactor system (Harbinger Biotechnology) at 37 ºC until OD₆₀₀ reached ~1.3. The culture was down-tempered to 18 ºC over a period of 1 hour before target expression was induced by addition of 0.5 mM IPTG. Expression was allowed to continue overnight and cells were harvested the following morning by centrifugation (4,700 x g, 10 min, 4 ºC). The resulting cell pellet (64.2 g wet cell weight) was resuspended in lysis buffer (2 mL/g cell pellet) supplemented with two tablets of Complete EDTA-free protease inhibitor (Roche Applied Science) and stored at -80 ºC.
Extraction buffers	Lysis buffer: 50 mM HEPES, 500 mM NaCl, 10% glycerol, 10 mM imidazole, 0.5 mM TCEP, pH 7.8
Extraction procedure	The cell suspension was quickly thawed and 4000 U Benzonase (Merck), 1 mM ATP and 1 mM MgCl₂ was added. Cells were disrupted by sonication (Vibra-Cell, Sonics) at 80% amplitude for 3 min effective time (pulsed 4s on, 4s off) and cell debris was removed by centrifugation (49,100 x g, 20 min, 4 ºC). The supernatant was decanted and filtered through a 0.45 µm flask filter.
Purification buffers	IMAC wash1 buffer: 30 mM HEPES, 500 mM NaCl, 10% glycerol, 10 mM imidazole, 0.5 mM TCEP, pH 7.5 IMAC wash2 buffer: 30 mM HEPES, 500 mM NaCl, 10% glycerol, 25 mM imidazole, 0.5 mM TCEP, pH 7.5 IMAC elution buffer: 30 mM HEPES, 500 mM NaCl, 10% glycerol, 500 mM imidazole, 0.5 mM TCEP, pH 7.5 Gel filtration (GF) buffer: 50 mM Na-citrate, 100 mM ammonium sulfate, 10% glycerol, 2 mM TCEP, pH 5.5
Purification procedure	Columns IMAC: Ni-charged 1 mL HiTrap Chelating HP (GE Healthcare) Gel filtration column: HiLoad 16/60 Superdex 200 Prep Grade (GE Healthcare) Procedure Purification of the protein was performed on an ÄKTAprime system (GE Healthcare). The filtered lysate was divided into two halves and loaded onto two separate HiTrap Chelating columns, pre-equilibrated with IMAC wash1 buffer. The columns were washed with IMAC wash1 buffer followed by IMAC wash2 buffer and the protein was eluted with IMAC elution buffer. Due to precipitation, the samples were diluted in GF-buffer and 1-10 mM of ATP and MgCl₂ was added. Tag removal The N-terminal histidine tag was proteolytically removed by incubating approximately 25% of the protein sample (~8 mg/mL in 5 mL) with His-tagged TEV protease at a molar ratio of 50:1 at 20 ºC overnight. The proteolytic reaction went to completion, as judged by SDS-PAGE. Prior to purification, columns were equilibrated with IMAC wash1 buffer (without imidazole) and gel filtration buffer, respectively. Target protein was purified from tag and protease by passing the reaction mixture over a Ni-charged HiTrap Chelating HP column (GE Healthcare). The protein was recovered from flow through and fresh TCEP was added to a final concentration of 2 mM. The protein was subsequently concentrated using an Amicon Ultra-15 centrifugal filter device, 10,000 NMWL (Millipore) and loaded onto the gel filtration column. Fractions containing the target protein were pooled and concentrated to 31.2 mg/mL in a volume of 0.2 mL. The identity of the protein was confirmed by mass spectrometry.
Crystallization	Crystals were obtained by the sitting drop vapour diffusion method in a 96-well plate. 0.2 µl protein solution (diluted to 20 mg/mL) including 2.5 mM ATP and 2.5 mM MgCl₂, was mixed with 0.1 µl of well solution consisting of 0.1 M bis-Tris pH 5.5, 0.2 M ammonium acetate and 25% PEG 3350. The plate was incubated at 20 ºC and crystals appeared within 12 days. The crystals were quickly transferred to a cryo solution consisting of well solution complemented with 15% glycerol, and flash frozen in liquid nitrogen.
Data collection	Diffraction data was collected at beamline ID 14-2 at the ESRF synchrotron radiation facility in Grenoble, France. Data was indexed and integrated in space group P4322 with the XDS package.
Data processing	The structure was solved by MR using PDB entry: 2CE7 - metalloprotease FtsH from Thermotoga maritima with Molrep. The asymmetric unit contains one protein monomer. The cell dimensions are a=b=57.20 Å c=155.22 Å. Refmac5 was used for refinement and Coot for model building. TLS restrained refinement using 3 TLS groups was used in the refinement process. The TLS groups were selected using the tlsmd server http://skuld.bmsc.washington.edu/~tlsmd/. Data in the interval 39.13-2.22Å resolution was used and at the end of the refinement the R values were: R= 20.9% and Rfree= 26.2%. Coordinates for the crystal structure were deposited in the Protein Data Bank, accession code 2QZ4.