3F2O

Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1 (SPSB1) in complex with a 20-residue VASA peptide

Summary for 3F2O

• Entry DOI: 10.2210/pdb3f2o/pdb
• Descriptor: SPRY domain-containing SOCS box protein 1, 20-mer peptide from ATP-dependent RNA helicase vasa (3 entities in total)
• Functional Keywords: apoptosis, nucleus, transcription regulation, sgc, structural genomics consortium, phosphoprotein, ubl conjugation pathway, atp-binding, developmental protein, differentiation, helicase, hydrolase, nucleotide-binding, oogenesis, apoptosis-hydrolase complex, apoptosis/hydrolase
• Biological source: Homo sapiens (Human); More
• Cellular location: Cytoplasm (Probable): Q96BD6; Cytoplasm: P09052
• Total number of polymer chains: 4
• Total formula weight: 58057.24

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.,Structural Genomics Consortium (SGC) (deposition date: 2008-10-30, release date: 2008-12-09, Last modification date: 2023-11-01)

Primary citation

Filippakopoulos, P.,Low, A.,Sharpe, T.D.,Uppenberg, J.,Yao, S.,Kuang, Z.,Savitsky, P.,Lewis, R.S.,Nicholson, S.E.,Norton, R.S.,Bullock, A.N.
Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4.
J.Mol.Biol., 401:389-402, 2010

PubMed Abstract: The mammalian SPRY domain- and SOCS box-containing proteins, SPSB1 to SPSB4, belong to the SOCS box family of E3 ubiquitin ligases. Substrate recognition sites for the SPRY domain are identified only for human Par-4 (ELNNNL) and for the Drosophila orthologue GUSTAVUS binding to the DEAD-box RNA helicase VASA (DINNNN). To further investigate this consensus motif, we determined the crystal structures of SPSB1, SPSB2, and SPSB4, as well as their binding modes and affinities for both Par-4 and VASA. Mutation of each of the three Asn residues in Par-4 abrogated binding to all three SPSB proteins, while changing EL to DI enhanced binding. By comparison to SPSB1 and SPSB4, the more divergent protein SPSB2 showed only weak binding to Par-4 and was hypersensitive to DI substitution. Par-4((59-77)) binding perturbed NMR resonances from a number of SPSB2 residues flanking the ELNNN binding site, including loop D, which binds the EL/DI sequence. Although interactions with the consensus peptide motif were conserved in all structures, flanking sites in SPSB2 were identified as sites of structural change. These structural changes limit high-affinity interactions for SPSB2 to aspartate-containing sequences, whereas SPSB1 and SPSB4 bind strongly to both Par-4 and VASA peptides.

PubMed: 20561531
DOI: 10.1016/j.jmb.2010.06.017

Experimental method

X-RAY DIFFRACTION (2.05 Å)