Human SPRY domain-containing SOCS box protein SSB-1 in complex with peptide

Target ID:

SPSB1A

Aliases:

SPSB1SSB-1SSB1

Deposition Date:

Thursday 30th October 2008

Families:

SOCS-box-containingUbiquitin Related BiologyUbiquitylation - E3 Ligases

Related Diseases:

Signalling

Structure type:

protein-ligand

Download Coordinates:

3F2O

Authors:

Filippakopoulos, P., Sharpe, T., Keates, T., Murray, J.W., Savitsky, P., Roos, A., Pike, A.C.W., Von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Bullock, A.

Site:

Oxford

ICM Datapack:

ICM Datapack

3F2O

tabs

Structure Details

Human SPRY-domain-containing SOCS box protein 1 (SPSB1 or SSB-1) belongs to a family of four proteins containing an N-terminal SPRY (or B30.2) domain and a C-terminal SOCS box (SPSB1-4). The SOCS box functions as an adaptor domain that binds ElonginBC and mediates further assembly with cullin ubiquitin ligases. The SPRY domain was first identified in the dual-specificity kinase splA and ryanodine receptors and is proposed to function as a protein-protein recognition domain. Several human diseases arise from mutations in genes coding for SPRY domain containing proteins, for example mutations in the MEFV gene are associated with familial Mediterranean fever.

SPSB1 is expressed in the ovary in granulosa cells at all stages of follicular development and is therefore proposed to regulate granulosa cell physiology. The SPSB1 SPRY domain has been shown to bind the MET receptor tyrosine kinase and to regulate the HGF-induced Erk-Elk-1-SRE pathway. It is highly conserved with the Drosophila homologue Gustavus for which structures have defined interactions with ElonginBC and an Asp-Ile-Asn-Asn-Asn-Asn recognition motif from the RNA helicase VASA. Here we determined the 2.0 Å crystal structure of human SPSB1 in complex with the Gustavus ligand VASA.

Materials and Methods

Entry Clone Source: MGC

Entry Clone Accession: IMAGE:3916157

SGC Construct ID: SPSB1A-c008

GenBank GI number: gi|18141316

Vector: pNIC28-Bsa4. Details [PDF ]; Sequence [ FASTA ] or [ GenBank ]

Tags and additions: Tag sequence:
mhhhhhhssgvdlgtenlyfq*s(m) TEV-cleavable (*) N-terminal his6 tag.

Final protein sequence:
mhhhhhhssgvdlgtenlyfq*smQELQG
LDYCKPTRLDLLLDMPPVSYDVQLLHSWN
NNDRSLNVFVKEDDKLIFHRHPVAQSTDA
IRGKVGYTRGLHVWQITWAMRQRGTHAVV
GVATADAPLHSVGYTTLVGNNHESWGWDL
GRNRLYHDGKNQPSKTYPAFLEPDETFIV
PDSFLVALDMDDGTLSFIVDGQYMGVAFR
GLKGKKLYPVVSAVWGHCEIRMRYLNGLD
PE

Host: BL21(DE3)-R3-pRARE2

Growth medium, induction protocol: Starter cultures in LB media (50 ml LB, 50 µg/ml kanamycin/ 34 µg/ml chloramphenicol) were inoculated from a glycerol stock and grown overnight. Three flasks containing 1L LB/antiobiotic media were each inoculated with 10 ml of overnight culture and grown at 37°C, 160 rpm until OD₆₀₀ = 0.5. The temperature was then reduced to 18°C at which point protein expression was induced with 0.5 mM IPTG (final concentration). Cells were harvested the following morning by centrifugation (15 min, 5000rpm, 4°C). The pellets were each resuspended in 40 ml binding buffer and frozen at ‑20°C. Binding buffer: 50mM HEPES pH 7.5; 500 mM NaCl; 5 mM imidazole, 5% glycerol.

Extraction method: Frozen pellets were thawed and fresh 1 mM PMSF, 0.5 mM TCEP, 10 mM L-arginine, 10 mM L-glutamate were added. Cells were lysed using a C5 high pressure homogeniser. DNA was precipitated by addition of PEI to a final concentration of 0.15%. The lysate was then centrifuged at 16,500 rpm for 60 minutes and the supernatant collected for purification.

Protein Purification, Column 1: IMAC Sepharose 6 Fast Flow resin, placed in series:
Column 1: Ni-affinity. Ni-sepharose (Amersham), 5 ml of 50% slurry in 1.5 x 10 cm column, washed with binding buffer.

Procedure: The soluble lysate was loaded by gravity flow on the Ni-sepharose column. The column was then washed with 100 ml wash buffer under gravity flow. The protein was eluted by applying 5-ml portions of elution buffer with increasing concentration of imidazole (50 mM, 100 mM, 150 mM and 250 mM); fractions were collected until essentially all protein was eluted. 10 mM DTT was added for overnight storage together with TEV protease for cleavage of the N-terminal hexahistidine tag.

Buffers: Binding buffer: 50 mM HEPES pH 7.5, 500 mM NaCl, 5 mM imidazole, 5% glycerol; Wash buffer: 50 mM HEPES pH 7.5, 500 mM NaCl, 30 mM Imidazole, 5% glycerol; Elution buffer: 50 mM HEPES pH 7.5, 500 mM NaCl, 50 to 250 mM Imidazole , 5% Glycerol.

Enzymatic treatment: Protein containing fractions were pooled and the His‑tag cleaved using TEV protease (reaction proceeded overnight at 4°C).

Column 2: Gel Filtration, HiLoad 16/60 Superdex 75 prep grade column run on an AKTA-express system.

Buffers: Gel Filtration Buffer: 25mM Hepes pH 7.5, 300 mM NaCl.

Procedure (Gel Filtration): The protein solution was concentrated to 3ml using a 5 kD MWCO Amicon Ultra concentrator. Protein was injected onto a pre-equilibrated gel filtration column and run at a flow rate of 1.0 ml/min. Fractions containing SPSB1 were pooled and mixed with 10 mM DTT for overnight storage.

Column 4: MonoQ ion exchange (Amersham)

Procedure: A further clean up step was performed to remove co-purifying proteins. SPSB1 from gel filtration was diluted with 50 mM HEPES pH 7.5 and loaded onto a 1 ml monoQ anion exchange column equilibrated in the same buffer. A linear elution gradient was run from 20-400 mM NaCl over 60 ml collecting 0.75 ml fractions. SPSB1 containing fractions were pooled and the buffer adjusted to 20 mM HEPES pH 7.5, 100 mM NaCl, 10 mM Arg/Glu, 10 mM DTT during concentration in a 5 kD MWCO Amicon Ultra concentrator.

Buffer A: 50 mM HEPES pH 7.5; Buffer B: 50 mM HEPES pH 7.5, 1M NaCl

Concentration: Protein was concentrated to 4 mg/ml determined by UV absorbance at 280 nm using an extinction coefficient of 46410 M-1cm-1. 1mM VASA peptide (DINNNNNIVEDVERKREFYI) was added prior to crystallization. The sample was centrifuged at 14 krpm for 10 minutes to remove any insoluble material.

Mass spectrometry characterization: LC- ESI -MS TOF. Expected mass (after TEV cleavage): 24029 Da. The expected mass was observed.

Crystallization: Crystals were obtained using the vapour diffusion method by mixing 666 nl of the concentrated protein (4 mg/ml) with 333 nl of a well solution containing the following components: 0.2M NaCl, 0.1M BisTris pH 5.5, 25% PEG 3350. Crystallization experiments were setup at 4 degrees C.

Data Collection: Crystals were cryo-protected using the well solution supplemented with an additional 20% ethylene glycol and flash frozen in liquid nitrogen. Diffraction data were collected from a single crystal at the SLS-X10 beamline. The structure was solved by molecular replacement and refined to 2.05 Å.

References

Masters, S.L., Yao, S, Willson, T.A., Zhang, J.G., Palmer, K.R., Smith, B.J., Babon, J.J., Nicola, N.A., Norton, R.S., Nicholson, S.E. (2006). The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4-binding residues. Nat Struct Mol Biol. 13, 77-84.

Wang, D., Li, Z., Messing, E.M., and Wu, G. (2005). The SPRY domain-containing SOCS box protein 1 (SSB-1) interacts with MET and enhances the hepatocyte growth factor-induced Erk-Elk-1-serum response element pathway. The Journal of Biological Chemistry 280, 16393-16401.

Woo, J.S., Suh, H.Y., Park, S.Y., and Oh, B.H. (2006). Structural basis for protein recognition by B30.2/SPRY domains. Molecular cell 24, 967-976.

Xing, Y., Gosden, R., Lasko, P., and Clarke, H. (2006). Murine homologues of the Drosophila gustavus gene are expressed in ovarian granulosa cells. Reproduction (Cambridge, England) 131, 905-915.