Structural basis of semaphorin–plexin signalling (original) (raw)

• Kruger, R. P., Aurandt, J. & Guan, K. L. Semaphorins command cells to move. Nature Rev. Mol. Cell Biol. 6, 789–800 (2005)
  Article CAS Google Scholar
• Tamagnone, L. et al. Plexins are a large family of receptors for transmembrane, secreted, and GPI-anchored semaphorins in vertebrates. Cell 99, 71–80 (1999)
  Article CAS Google Scholar
• Suto, F. et al. Interactions between plexin-A2, plexin-A4, and semaphorin 6A control lamina-restricted projection of hippocampal mossy fibers. Neuron 53, 535–547 (2007)
  Article CAS Google Scholar
• Kolodkin, A. L., Matthes, D. J. & Goodman, C. S. The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules. Cell 75, 1389–1399 (1993)
  Article CAS Google Scholar
• Love, C. A. et al. The ligand-binding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D. Nature Struct. Biol. 10, 843–848 (2003)
  Article CAS Google Scholar
• Antipenko, A. et al. Structure of the semaphorin-3A receptor binding module. Neuron 39, 589–598 (2003)
  Article CAS Google Scholar
• Winberg, M. L. et al. Plexin A is a neuronal semaphorin receptor that controls axon guidance. Cell 95, 903–916 (1998)
  Article CAS Google Scholar
• Capparuccia, L. & Tamagnone, L. Semaphorin signaling in cancer cells and in cells of the tumor microenvironment–two sides of a coin. J. Cell Sci. 122, 1723–1736 (2009)
  Article CAS Google Scholar
• Korostylev, A. et al. A functional role for semaphorin 4D/plexin B1 interactions in epithelial branching morphogenesis during organogenesis. Development 135, 3333–3343 (2008)
  Article CAS Google Scholar
• Kerjan, G. et al. The transmembrane semaphorin Sema6A controls cerebellar granule cell migration. Nature Neurosci. 8, 1516–1524 (2005)
  Article CAS Google Scholar
• Renaud, J. et al. Plexin-A2 and its ligand, Sema6A, control nucleus-centrosome coupling in migrating granule cells. Nature Neurosci. 11, 440–449 (2008)
  Article CAS Google Scholar
• He, H., Yang, T., Terman, J. R. & Zhang, X. Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration. Proc. Natl Acad. Sci. USA 106, 15610–15615 (2009)
  Article ADS Google Scholar
• Tong, Y. et al. Structure and function of the intracellular region of the plexin-B1 transmembrane receptor. J. Biol. Chem. 284, 35962–35972 (2009)
  Article CAS Google Scholar
• Takahashi, T. & Strittmatter, S. M. Plexina1 autoinhibition by the plexin sema domain. Neuron 29, 429–439 (2001)
  Article CAS Google Scholar
• Takahashi, T. et al. Plexin-neuropilin-1 complexes form functional semaphorin-3A receptors. Cell 99, 59–69 (1999)
  Article CAS Google Scholar
• Oinuma, I., Katoh, H. & Negishi, M. Molecular dissection of the semaphorin 4D receptor plexin-B1-stimulated R-Ras GTPase-activating protein activity and neurite remodeling in hippocampal neurons. J. Neurosci. 24, 11473–11480 (2004)
  Article CAS Google Scholar
• Tong, Y. et al. Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J. Biol. Chem. 282, 37215–37224 (2007)
  Article CAS Google Scholar
• Gherardi, E., Love, C. A., Esnouf, R. M. & Jones, E. Y. The sema domain. Curr. Opin. Struct. Biol. 14, 669–678 (2004)
  Article CAS Google Scholar
• Stamos, J., Lazarus, R. A., Yao, X., Kirchhofer, D. & Wiesmann, C. Crystal structure of the HGF β-chain in complex with the Sema domain of the Met receptor. EMBO J. 23, 2325–2335 (2004)
  Article CAS Google Scholar
• Niemann, H. H. et al. Structure of the human receptor tyrosine kinase met in complex with the Listeria invasion protein InlB. Cell 130, 235–246 (2007)
  Article CAS Google Scholar
• Koppel, A. M., Feiner, L., Kobayashi, H. & Raper, J. A. A 70 amino acid region within the semaphorin domain activates specific cellular response of semaphorin family members. Neuron 19, 531–537 (1997)
  Article CAS Google Scholar
• Müller, K. M., Arndt, K. M. & Pluckthun, A. Model and simulation of multivalent binding to fixed ligands. Anal. Biochem. 261, 149–158 (1998)
  Article Google Scholar
• Klostermann, A., Lohrum, M., Adams, R. H. & Puschel, A. W. The chemorepulsive activity of the axonal guidance signal semaphorin D requires dimerization. J. Biol. Chem. 273, 7326–7331 (1998)
  Article CAS Google Scholar
• Koppel, A. M. & Raper, J. A. Collapsin-1 covalently dimerizes, and dimerization is necessary for collapsing activity. J. Biol. Chem. 273, 15708–15713 (1998)
  Article CAS Google Scholar
• Turner, L. J. & Hall, A. Plexin-induced collapse assay in COS cells. Methods Enzymol. 406, 665–676 (2006)
  Article CAS Google Scholar
• Merte, J. et al. A forward genetic screen in mice identifies Sema3A(K108N), which binds to neuropilin-1 but cannot signal. J. Neurosci. 30, 5767–5775 (2010)
  Article CAS Google Scholar
• Liu, H. et al. Structural basis of Semaphorin-Plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1. Cell 142, 749–761 (2010)
  Article CAS Google Scholar
• Toyofuku, T. et al. FARP2 triggers signals for Sema3A-mediated axonal repulsion. Nature Neurosci. 8, 1712–1719 (2005)
  Article CAS Google Scholar
• Gherardi, E. et al. Structural basis of hepatocyte growth factor/scatter factor and MET signalling. Proc. Natl Acad. Sci. USA 103, 4046–4051 (2006)
  Article ADS CAS Google Scholar
• Aricescu, A. R., Lu, W. & Jones, E. Y. A time- and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr. D 62, 1243–1250 (2006)
  Article CAS Google Scholar
• Chang, V. T. et al. Glycoprotein structural genomics: solving the glycosylation problem. Structure 15, 267–273 (2007)
  Article CAS Google Scholar
• Reeves, P. J., Callewaert, N., Contreras, R. & Khorana, H. G. Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl Acad. Sci. USA 99, 13419–13424 (2002)
  Article ADS CAS Google Scholar
• Walter, T. S. et al. A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr. D 61, 651–657 (2005)
  Article CAS Google Scholar
• Mayo, C. J. et al. Benefits of automated crystallization plate tracking, imaging, and analysis. Structure 13, 175–182 (2005)
  Article CAS Google Scholar
• Otwinowski, Z. & Minor, W. Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
  Article CAS Google Scholar
• Leslie, A. G. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography 26, (1992)
• Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)
  Article CAS Google Scholar
• CCP4. The _CCP_4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)
• McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)
  Article CAS Google Scholar
• Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)
  Article CAS Google Scholar
• Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463 (1999)
  Article CAS Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
  Article CAS Google Scholar
• Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D 62, 1002–1011 (2006)
  Article CAS Google Scholar
• Blanc, E. et al. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr. D 60, 2210–2221 (2004)
  Article CAS Google Scholar
• Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)
  Article ADS Google Scholar
• Stuart, D. I., Levine, M., Muirhead, H. & Stammers, D. K. Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 Å. J. Mol. Biol. 134, 109–142 (1979)
  Article CAS Google Scholar
• Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001)
  Article ADS CAS Google Scholar
• Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)
  Article CAS Google Scholar
• Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007)
  Article CAS Google Scholar
• Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999)
  Article CAS Google Scholar
• Landau, M. et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33, W299–W302 (2005)
  Article ADS CAS Google Scholar
• O’Callaghan C. A. et al. BirA enzyme: production and application in the study of membrane receptor-ligand interactions by site-specific biotinylation. Anal. Biochem. 266, 9–15 (1999)
  Article Google Scholar
• Trombetta, E. S. & Parodi, A. J. Quality control and protein folding in the secretory pathway. Annu. Rev. Cell Dev. Biol. 19, 649–676 (2003)
  Article CAS Google Scholar
• Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78, 1606–1619 (2000)
  Article ADS CAS Google Scholar