Proteopedia

3f2o

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

Structural highlights

3f2o is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:SPSB1, SSB1 (Homo sapiens)
Resources:FirstGlance, OCA, RCSB, PDBsum

Function

[SPSB1_HUMAN] Probable substrate recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.[1] [VASA_DROME] Involved in translational control mechanisms operating in early stages of oogenesis. Required maternally in many stages of oogenesis, including cystocyte differentiation, oocyte differentiation, and specification of anterior-posterior polarity in the developing cysts. Essential for the formation and/or structural integrity of perinuclear nuage particles.[2] [3] [4] [5] [6] [7] [8] [9]

Evolutionary Conservation

 

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4.,Filippakopoulos P, Low A, Sharpe TD, Uppenberg J, Yao S, Kuang Z, Savitsky P, Lewis RS, Nicholson SE, Norton RS, Bullock AN J Mol Biol. 2010 Aug 20;401(3):389-402. Epub 2010 Jun 16. PMID:20561531[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Kamura T, Maenaka K, Kotoshiba S, Matsumoto M, Kohda D, Conaway RC, Conaway JW, Nakayama KI. VHL-box and SOCS-box domains determine binding specificity for Cul2-Rbx1 and Cul5-Rbx2 modules of ubiquitin ligases. Genes Dev. 2004 Dec 15;18(24):3055-65. PMID:15601820 doi:http://dx.doi.org/10.1101/gad.1252404
  2. ↑ Lasko PF, Ashburner M. The product of the Drosophila gene vasa is very similar to eukaryotic initiation factor-4A. Nature. 1988 Oct 13;335(6191):611-7. PMID:3140040 doi:http://dx.doi.org/10.1038/335611a0
  3. ↑ Hay B, Jan LY, Jan YN. A protein component of Drosophila polar granules is encoded by vasa and has extensive sequence similarity to ATP-dependent helicases. Cell. 1988 Nov 18;55(4):577-87. PMID:3052853
  4. ↑ Liang L, Diehl-Jones W, Lasko P. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development. 1994 May;120(5):1201-11. PMID:8026330
  5. ↑ Styhler S, Nakamura A, Swan A, Suter B, Lasko P. vasa is required for GURKEN accumulation in the oocyte, and is involved in oocyte differentiation and germline cyst development. Development. 1998 May;125(9):1569-78. PMID:9521895
  6. ↑ Carrera P, Johnstone O, Nakamura A, Casanova J, Jackle H, Lasko P. VASA mediates translation through interaction with a Drosophila yIF2 homolog. Mol Cell. 2000 Jan;5(1):181-7. PMID:10678180
  7. ↑ Styhler S, Nakamura A, Lasko P. VASA localization requires the SPRY-domain and SOCS-box containing protein, GUSTAVUS. Dev Cell. 2002 Dec;3(6):865-76. PMID:12479811
  8. ↑ Liu N, Dansereau DA, Lasko P. Fat facets interacts with vasa in the Drosophila pole plasm and protects it from degradation. Curr Biol. 2003 Oct 28;13(21):1905-9. PMID:14588248
  9. ↑ Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054
  10. ↑ Filippakopoulos P, Low A, Sharpe TD, Uppenberg J, Yao S, Kuang Z, Savitsky P, Lewis RS, Nicholson SE, Norton RS, Bullock AN. Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4. J Mol Biol. 2010 Aug 20;401(3):389-402. Epub 2010 Jun 16. PMID:20561531 doi:10.1016/j.jmb.2010.06.017

3f2o, resolution 2.05Å

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