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3D Repertoire Publications Press

Publications resulting from the work carried out under 3D Repertoire

The work carried out in the following publications was partly funded by the European Commission under FP6, contract LSHG-CT-2005-512028.

  • 2008
    • Janin, J. Biochemistry. Dicey assemblies. Science 319, 165-6 (2008).
    • Graille, M., Chaillet, M. & van Tilbeurgh, H. Structure of yeast Dom34: a protein related to translation termination factor eRF1 and involved in No-Go decay. J Biol Chem (2008).
    • Leulliot, N. et al. Structure of the yeast tRNA m7G methylation complex. Structure 16, 52-61 (2008).
  • 2007
    • Campos-Olivas, R., Sánchez, R., Torres, D., and Blanco, F.J. (2007) “Backbone assignment of the 98kDa homotrimeric yeast PCNA ring”. J. Biomol NMR 38, 137.
    • Gallego, O. and Gavin A.C. (2007). “New perspectives on an old disease: proteomics in cancer research”. Genome Biol. 8, 303-306.
    • Nickell, S., Mihalache, O., Beck, F., Korinek, A., Baumeister, W. and Plitzko, J.M. (2007) Automated cryoelectron microscopy of "single particles" applied to the 26S proteasome. FEBS Letters 581, 15 2751–2756.
    • Musacchio, A., & Salmon, E.D. (2007) The spindle assembly checkpoint in space and time. Nature Rev Mol Cell Biol, 8, 379-93.
    • Ciferri, C., Musacchio, A. & Petrovic, A. (2007) The Ndc80 complex: Hub of kinetochore activity, FEBS Lett. 581, 2862-9.
    • Boskovic, J., Coloma, J., Aparicio, T., Zhou, M., Robinson, C.V., Mendez, J., Montoya, G. (2007) Molecular architecture of the human GINS complex. EMBO Rep. 2007 Jun 8
    • Fernandez-Tornero, C., Böttcher, B., Riva, M., Carles, C., Steuerwald, U., Ruigrok, R.W., Sentenac, A., Müller, C.W. and Schoehn, G. (2007) Insights into transcription initiation and termination from the electron microscopy structure of yeast RNA polymerase III. Mol Cell, 25, 813-823.
    • Leulliot, N., Godin, K.S., Hoareau-Aveilla, C., Quevillon-Cheruel, S., Varani, G., Henry, Y., van Tilbeurgh, H. (2007) The Box H/ACA RNP Assembly Factor Naf1p Contains a Domain Homologous to Gar1p Mediating its Interaction with Cbf5p. J Mol Biol. Aug 31;371(5):1338-53.
    • Lorentzen, E., Dziembowski, A., Lindner, D., Seraphin, B. and Conti, E. (2007) RNA channelling by the archaeal exosome. EMBO Rep. 8, 470-476.
    • Bahadur, R.P., Rodier, F., & Janin, J. (2007) A dissection of protein-protein interfaces in icosahedral virus capsids. J. Mol. Biol. 367, 574-590.
    • Betts, M.J., Russell, R.B. (2007) The hard cell: from proteomics data to a whole cell model. FEBS Lett. 581, 2870–2876, 2007
    • Chesneau, A.C., Yumerefendi, H. and Hart, D.J. Impact of protein expression methodologies on structural proteomics. Structural Proteomics (2007).
    • Jeyaprakash, A.A. et al. Structure of a Survivin-Borealin-INCENP core complex reveals how chromosomal passengers travel together. Cell 131, 271-85 (2007).
    • Robinson, C.V., Sali, A. & Baumeister, W. The molecular sociology of the cell. Nature 450, 973-82 (2007).
    • Aloy, P. Shaping the future of interactome networks. Genome Biol 8, 316 (2007).
    • Karanasios, E., Simader, H., Panayotou, G., Suck, D. & Simos, G. Molecular determinants of the yeast Arc1p-aminoacyl-tRNA synthetase complex assembly. J Mol Biol 374, 1077-90 (2007).
    • Sirajuddin, M. et al. Structural insight into filament formation by mammalian septins. Nature 449, 311-5 (2007).
    • Kastner, B. et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat Methods 5, 53-5 (2008).
    • Mapelli, M. & Musacchio, A. MAD contortions: conformational dimerization boosts spindle checkpoint signaling. Curr Opin Struct Biol 17, 716-25 (2007).
    • Hecker, A. et al. An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res 35, 6042-51 (2007).
    • Wendler, P. et al. Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104. Cell 131, 1366-77 (2007).
    • Martin-Benito, J. et al. Divergent substrate-binding mechanisms reveal an evolutionary specialization of eukaryotic prefoldin compared to its archaeal counterpart. Structure 15, 101-10 (2007).
    • Martin-Benito, J. et al. The inter-ring arrangement of the cytosolic chaperonin CCT. EMBO Rep 8, 252-7 (2007).
    • Janin, J. The targets of CAPRI rounds 6-12. Proteins 69, 699-703 (2007).
    • Bahadur, R.P. & Janin, J. Residue conservation in viral capsid assembly. Proteins (2007).
    • Devos, D. & Russell, R.B. A more complete, complexed and structured interactome. Curr Opin Struct Biol 17, 370-7 (2007).
    • Moelleken, J. et al. Differential localization of coatomer complex isoforms within the Golgi apparatus. Proc Natl Acad Sci U S A 104, 4425-30 (2007).
    • Janin, J. & Wodak, S. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure 15, 755-9 (2007).
    • Janin, J. Structural genomics: winning the second half of the game. Structure 15, 1347-9 (2007).
  • 2006
    • Aloy, P., and Russell, R. B. (2006). Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7, 188-197.
    • Benesch, J. L., and Robinson, C. V. (2006). Mass spectrometry of macromolecular assemblies: preservation and dissociation. Curr Opin Struct Biol 16, 245-251.
    • Bravo, J., and Aloy, P. (2006). Target selection for complex structural genomics. Curr Opin Struct Biol 16, 385-392.
    • Campos-Olivas, R., Sanchez, R., Torres, D., and Blanco, F. J. (2006). Backbone assignment of the 98 kDa homotrimeric yeast PCNA ring. J Biomol NMR.
    • DeLuca, J. G., Gall, W. E., Ciferri, C., Cimini, D., Musacchio, A., and Salmon, E. D. (2006). Kinetochore microtubule dynamics and attachment stability are regulated by Hec1. Cell 127, 969-982.
    • Devos, D., Kalinina, O. V., and Russell, R. B. (2006). Harry Potter and the structural biologist's (Key)stone. Genome Biol 7, 333.
    • Dopazo, J., and Aloy, P. (2006). Discovery and hypothesis generation through bioinformatics. Genome Biol 7, 307.
    • Gabel, F., Simon, B., and Sattler, M. (2006). A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints. Eur Biophys J 35, 313-327.
    • Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dumpelfeld, B., et al. (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636.
    • Hernandez, H., Dziembowski, A., Taverner, T., Seraphin, B., and Robinson, C. V. (2006). Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep 7, 605-610.
    • Heurgue-Hamard, V., Graille, M., Scrima, N., Ulryck, N., Champ, S., van Tilbeurgh, H., and Buckingham, R. H. (2006). The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. J Biol Chem 281, 36140-36148.
    • Itzhaki, Z., Akiva, E., Altuvia, Y., and Margalit, H. (2006). Evolutionary conservation of domain-domain interactions. Genome Biol 7, R125.
    • Lariviere, L., Geiger, S., Hoeppner, S., Rother, S., Strasser, K., and Cramer, P. (2006). Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nat Struct Mol Biol 13, 895-901.
    • Lorentzen, E., and Conti, E. (2006). The exosome and the proteasome: nano-compartments for degradation. Cell 125, 651-654.
    • Mylona, A., Fernandez-Tornero, C., Legrand, P., Haupt, M., Sentenac, A., Acker, J., and Müller, C. W. (2006). Structure of the tau60/Delta tau91 subcomplex of yeast transcription factor IIIC: insights into preinitiation complex assembly. Mol Cell 24, 221-232.
    • Neduva, V., and Russell, R. B. (2006). Peptides mediating interaction networks: new leads at last. Curr Opin Biotechnol 17, 465-471.
    • Pimienta, G., Gabel, F., Zanier, K., Conti, E., and Sattler, M. (2006). Chemical Shift Backbone Assignments of TAP-N, the 31 kDa Cargo-binding Region of the Protein TAP. J Biomol NMR 36 Suppl 5, 23.
    • Romier, C., Ben Jelloul, M., Albeck, S., Buchwald, G., Busso, D., Celie, P. H., Christodoulou, E., De Marco, V., van Gerwen, S., Knipscheer, P., et al. and Perrakis, A. (2006). Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies. Acta Crystallogr D Biol Crystallogr 62, 1232-1242.
    • Schafer, T., Maco, B., Petfalski, E., Tollervey, D., Böttcher, B., Aebi, U., and Hurt, E. (2006). Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit. Nature 441, 651-655.
    • Simader, H., Hothorn, M., Kohler, C., Basquin, J., Simos, G., and Suck, D. (2006a). Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes. Nucleic Acids Res 34, 3968-3979.
    • Simader, H., Hothorn, M., and Suck, D. (2006b). Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold. Acta Crystallogr D Biol Crystallogr 62, 1510-1519.
    • Simader, H., and Suck, D. (2006). Expression, purification, crystallization and preliminary phasing of the heteromerization domain of the tRNA-export and aminoacylation cofactor Arc1p from yeast. Acta Crystallograph Sect F Struct Biol Cryst Commun 62, 346-349.
  • 2005
    • Aloy, P., Pichaud, M., and Russell, R. B. (2005). Protein complexes: structure prediction challenges for the 21st century. Curr Opin Struct Biol 15, 15-22.
    • Aloy, P., and Russell, R. B. (2005). Structure-based systems biology: a zoom lens for the cell. FEBS Lett 579, 1854-1858.
    • Baumli, S., Hoeppner, S., and Cramer, P. (2005). A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J Biol Chem 280, 18171-18178.
    • Dube, P., Herzog, F., Gieffers, C., Sander, B., Riedel, D., Muller, S. A., Engel, A., Peters, J. M., and Stark, H. (2005). Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C. Mol Cell 20, 867-879.
    • Hoeppner, S., Baumli, S., and Cramer, P. (2005). Structure of the mediator subunit cyclin C and its implications for CDK8 function. J Mol Biol 350, 833-842.
    • Lorentzen, E., and Conti, E. (2005). Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol Cell 20, 473-481.
    • Lorentzen, E., Walter, P., Fribourg, S., Evguenieva-Hackenberg, E., Klug, G., and Conti, E. (2005). The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol 12, 575-581.
    • Ruotolo, B. T., Giles, K., Campuzano, I., Sandercock, A. M., Bateman, R. H., and Robinson, C. V. (2005). Evidence for macromolecular protein rings in the absence of bulk water. Science 310, 1658-1661.
    • Shah, P. K., Aloy, P., Bork, P., and Russell, R. B. (2005). Structural similarity to bridge sequence space: finding new families on the bridges. Protein Sci 14, 1305-1314.
    • Venzke, D., Domgall, I., Kocher, T., Fethiere, J., Fischer, S., and Böttcher, B. (2005). Elucidation of the stator organization in the V-ATPase of Neurospora crassa. J Mol Biol 349, 659-669.