Funded by EU Framework 6



Jobs I Contact
Home Complexes Structures Publications Workshops & Meetings Facilities & Methods Private
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.

  • 2010
    • Trowitzsch, S., Bieniossek, C., Nie, Y., Garzoni, F., Berger, I. (2010) “New eukaryotic expression tools for protein complex production.” J. Struct. Biol. J Struct Biol. Feb 21. [Epub ahead of print] (PubMed)
    • Koschubs T, Lorenzen K, Baumli S, Sandström S, Heck AJR, Cramer P, (2010) Preparation and topology of the Mediator middle module, Nucleic Acids Research, Jan 31. [Epub ahead of print] (PubMed)
    • Yumerefendi, H., Tarendeau, F., Mas, P. & Hart, DJ, (2010) ESPRIT: An automated, library-based method for mapping and soluble expression of protein domains from challenging targets, J Struct Biol. Mar 4. [Epub ahead of print] (PubMed)
    • A. Panjkovich and P. Aloy. “Predicting protein-protein interaction specificity through the integration of three-dimensional structural information and the evolutionary record of protein domains”. Mol BioSyst. (2010). 2010 Apr;6(4):741-9. (PubMed)
    • Simon B, Madl T, Mackereth CD, Nilges M, Sattler M (2010) An Efficient Protocol for NMR-Based Structure Determination of Protein Complexes in Solution. Angew Chem Int Ed Engl. Mar 8;49(11):1967-70. (PubMed)
    • Cook, A. and Conti, E. (2010). Nuclear export complexes in the frame. Curr Opin Struct Biol. 2010 Apr;20(2):247-52. (PubMed)
    • Dey S, Pal A, Chakrabarti P, Janin J (2010). The subunit interfaces of weakly associated homodimeric proteins. J. Mol. Biol. Apr 23;398(1):146-60. (PubMed)
  • 2009
    • Kühner S., van Noort V., Betts M.J., Leo-Macias A., Batisse C., Rode M., Yamada T., Maier T., Bader S., Beltran-Alvarez P., Castaño-Diez D., Chen W.H., Devos D., Güell Cargol M., Norambuena T., Racke I., Rybin V., Schmidt A., Yus E., Aebersold R., Herrmann R., Böttcher B., Frangakis A.S., Russell R.B., Serrano L., >Bork P. and Gavin A.C. (2009). Proteome organization in a genome-reduced bacterium. Science 326, 1235-1240. (PubMed)
    • Batisse, J., Batisse, C., Budd, A., Böttcher, B., and Hurt, E. (2009). Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure. J Biol Chem 284, 34911-34917. (PubMed)
    • Nie, Y., Viola, C., Bieniossek, C., Trowitzsch, S., Vijayachandran, L.S., Chaillet, M., Garzoni, F., & Berger, I. (2009) “Getting a Grip on Complexes” Curr. Genomics 10, 558-572.
    • Bieniossek, C., Nie, Y., Frey, D., Olieric, N., Schaffitzel, C., Collinson, I., Romier, C., Richmond, T.J., Steinmetz, M.O. & Berger, I. (2009) “Automated unrestricted multigene recombineering for multiprotein complex production” Nature Methods 6, 447-450. (PubMed)
    • Bieniossek, C. & Berger, I. (2009) “Towards eukaryotic structural complexomics” J. Struct. Funct. Genomics 10, 37-47. (PubMed)
    • Santaguida S & Musacchio A (2009) “The life and miracles of kinetochores”. EMBO Sep 2;28(17):2511-31. (PubMed)
    • Carulla N, Zhou M, Arimon M, Gairí M, Giralt E, Robinson CV, Dobson CM. (2009) Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation. Proc Natl Acad Sci U S A. May 12;106(19):7828-33 (PubMed)
    • Cook, A., Fukuhara, N., Jinek M. and Conti E. (2009). Structures of the tRNA export factor in the nuclear and cytosolic states. Nature, 461, 60-65. (PubMed)
    • Bonneau, F., Basquin, J., Ebert, J., Lorentzen E. and Conti E. (2009). The yeast exosome functions as a macromolecular caged to channel RNA substrates for degradation. Cell, 139, 547-559. (PubMed)
    • Wendler, P, Shorter, J, Snead, D, Plisson, C, Clare, DK, Lindquist, S, Saibil, HR (2009) Motor mechanism for protein threading through Hsp104. Mol. Cell 34, 81-92. (PubMed)
    • Stephan Nickell, Florian Beck, Sjors H.W. Scheres, Andreas Korinek, Friedrich Förster, Keren Lasker, Oana Mihalache, Na Sun, István Nagy, Andrej Sali, Jürgen M. Plitzko, Jose-Maria Carazo, Matthias Mann, Wolfgang Baumeister (2009) Insights into the molecular architecture of the 26S proteasome, PNAS, Vol. 106 No. 29, 11943-11947. (PubMed)
    • Friedrich Förster, Keren Lasker, Florian Beck, Stephan Nickell, Andrej Sali, Wolfgang Baumeister (2009) An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome, Biochemical and Biophysical Research Communications, Vol. 388, 228–233. (PubMed)
    • Cornelia Ulbrich, Meikel Diepholz, Jochen Baßler, Dieter Kressler, Brigitte Pertschy, Kyriaki Galani, Bettina Böttcher and Ed Hurt (2009) Mechanochemical Removal of Ribosome Biogenesis Factors from Nascent 60S Ribosomal Subunits; Cell Sep 4;138(5):911-22. (PubMed)
    • Friberg A, Corsini L, Mourao A, Sattler M. (2009) Structure and ligand binding of the extended Tudor domain of D. Melanogaster Tudor-SN. J. Mol. Biol. (2009) 387, 921–934 (PubMed)
    • Neufeld C, Filipp FV, Simon B, Neuhaus A, Schüller N, David C, Kooshapur H, Madl T, Erdmann R, Schliebs W, Wilmanns M, Sattler M. (2009) Structural basis for competitive interactions of Pex14 with the import receptors Pex5 and Pex19. EMBO J 28:745-54. (PubMed)
    • Corsini L, Hothorn M, Stier G, Rybin V, Scheffzek K, Gibson TJ, Sattler M. (2009) Dimerization and protein binding specificity of the U2AF homology motif (UHM) of the splicing factor Puf60. J Biol Chem, 284:630-9 (PubMed)
    • R. Mosca, C. Pons, J. Fernández-Recio and P. Aloy. “Pushing structural information into the yeast interactome by high-throughput protein docking experiments”. PLoS Comput Biol. (2009) 5(8):e1000490. (PubMed)
    • A. Stein, R.A. Pache, P. Bernardó, M. Pons and P. Aloy. “Dynamic interactions of proteins in complex networks: a more structured view”. FEBS J. (2009) 276(19):5390-405. (PubMed)
    • R.A. Pache, M.M. Babu and P. Aloy. “Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions”. BMC Syst Biol. (2009) 18;3:74. (PubMed)
    • A. Stein, A. Panjkovich and P. Aloy. “3did Update: domain-domain and peptide-mediated interactions of known 3D structure”. Nucleic Acids Res. (2009) 37:D300-4. (PubMed)
    • Janin J. “Basic principles of protein-protein interaction” in Computational Protein-Protein Interactions. G. Schreiber and R. Nussinov, ed., pp. 2-19, CRC Press, June 26, 2009.
    • Petsalaki E, Stark A, García-Urdiales E, Russell RB, (2009) Accurate prediction of peptide binding sites on protein surfaces, PLoS Comp. Biol, PLoS Comput Biol 5(3): e1000335. (PubMed)
    • Reubold TF, Wohlgemuth S, Eschenburg S., A new model for the transition of APAF-1 from inactive monomer to caspase-activating apoptosome, J. Biol. Chem. 2009, 284(47):32717-24. (PubMed)
    • Wodak, S.J., Pu, S., Vlasblom, J., Séraphin, B. (2009) Challenges and rewards of interaction proteomics. Mol Cell Proteomics. 8, 3-18. (PubMed)
    • Aparicio T, Guillou E, Coloma J, Montoya G, Méndez J. (2009) The human GINS complex associates with Cdc45 and MCM and is essential for DNA replication. Nucleic Acids Research, Apr;37(7):2087-95. (PubMed)
    • Koschubs T., Seizl M., Larivière L., Kurth F., Baumli S., Martin D.E., Cramer P. (2009). Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J Jan 7, 28(1):69-80. (PubMed)
    • Golas, M.M., Böhm, C., Sander, B. Effenberger, K. Brecht, M., Stark, H., Göringer, U. (2009) Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo. EMBO J, Mar 18;28(6):766-78. (PubMed)
    • Herzog, F., Primorac, I., Dube, P., Lenart, P., Sander, B., Mechtler, K., Stark, H., Peters, J.M. (2009) Structure of the anaphase promoting complex/cyclosome interacting with a mitotic checkpoint complex. Science, Mar 13;323(5920):1477-81. (PubMed)
    • Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.P., Pedersen, J.S., Birkedal, V., Besenbacher, F., Gothelf, K.V., Kjems, J. (2009) Self-assembly of a nano-scale DNA box with a controllable lid. Nature, May 7;459(7243):73-6. (PubMed)
    • Clare DK, Bakkes PJ, van Heerikhuizen H, van der Vies SM, Saibil HR. (2009) Chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature. Jan 1;457(7225):107-10. (PubMed)
    • Brooks MA, Dziembowski A, Quevillon-Cheruel S, Henriot V, Faux C, van Tilbeurgh H, Séraphin B. (2009) Structure of the yeast Pml1 splicing factor and its integration into the RES complex. Nucleic Acids Res. Jan;37(1):129-43. (PubMed)
  • 2008
    • Lebreton, A., Séraphin, B. (2008) Exosome-mediated quality control: substrate recruitment and molecular activity. BBA – Gene Regulatory Mechanisms 1779, 558–565. (PubMed)
    • Civril F, Musacchio A. (2008) Spindly attachments. Genes Dev. 22:2302-7. (PubMed)
    • Lebreton , A., R. Tomecki , Dziembowski A and B. Séraphin Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature, 2008 Dec 18;456(7224):993-6 (PubMed)
    • T Taverner, H Hernández, M Sharon, BT Ruotolo, D Matak-Vinkovic, D Devos, RB Russell, CV Robinson. (2008) Subunit architecture of intact protein complexes from mass spectrometry and homology modeling. Acc Chem Res 41: 617-627. (PubMed)
    • M Zhou, AM Sandercock, CS Fraser, G Ridlova, E Stephens, MR Schenauer, T Yokoi-Fong, JA Leary, JW Hershey, J Doudna, CV Robinson (2008) Mass Spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18139-44. (PubMed
    • Jonathan P. Schuermann, Jianwen Jiang, Jorge Cuéllar, Oscar Llorca, Liping Wang, Alexander B. Taylor, Borries Demeler, Kevin Morano, P. John Hart, José M. Valpuesta, Eileen M. Lafer and Rui Sousa (2008) “Structure of the Hsp110:Hsc70 Nucleotide Exchange Complex” Molecular Cell 31, 232-243 (selected by the Faculty of 1000). (PubMed)
    • Jorge Cuéllar, Jaime Martín-Benito, Sjors H.W. Scheres, Rui Sousa, Fernando Moro, Eduardo López-Viñas, Paulino Gómez-Puertas, Arturo Muga, José L. Carrascosa and José M. Valpuesta. (2008) “The structure of a CCT:Hsc70NBD complex suggests a mechanism for Hsp70 delivery of substrates to the chaperonin” Nat. Struct. Mol. Biol. 15, 858-864 (selected by the Faculty of 1000). (PubMed)
    • Lorentzen, E., Basquin, J., Tomecki, R., Dziembowski, A. and Conti, E. (2008). Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol Cell 29, 717-728. (PubMed)
    • Lorentzen, E., Basquin, J. and Conti, E. (2008). Structural organization of the RNA degrading exosome. Curr Opin Struct Biol. 2008 Dec;18(6):709-13. (PubMed)
    • Hecker A, Lopreiato R, Graille M, Collinet B, Forterre P, Libri D, van Tilbeurgh H. (2008) Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J. Aug 7. (PubMed)
    • Gabel F, Simon B, Nilges M, Petoukhov M, Svergun D, Sattler M. (2008) A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints. J Biomol NMR. 41, 199-208. (PubMed)
    • Rumpf J., Simon B., Jung N., Maritzen T., Haucke V., Sattler M., and Groemping Y. (2008) Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity. EMBO J 27, 558-69. (PubMed)
    • Clare DK, Stagg S, Quispe J, Farr GW, Horwich AL, Saibil HR (2008) Multiple states of a nucleotide-bound group 2 chaperonin. Structure 16:528-34 (PubMed)
    • Ciferri C., Pasqualato S., Screpanti E., Varetti G., Santaguida S., Dos Reis G., Maiolica A., Polka J., De Luca J.G., De Wulf P., Salek M., Rappsilber J., Moores C.A., Salmon E.D. and Musacchio A. (2008) Implications for kinetochore-microtubule attachment from the structure of an engineered Ndc80 complex. Cell 133: 427-39 (PubMed)
    • Cristodero, M., Böttcher, B., Diepholz, M., Scheffzek, K. and Clayton, C. (2008) The Leishmania tarentolae exosome: purification and structural analysis by electron microscopy. Mol Biochem Parasitol, 159, 24-29.
    • Diepholz, M., Börsch, M. and Böttcher, B. (2008) Structural organization of the V-ATPase and its implications for regulatory assembly and disassembly. Biochem Soc Trans, 36, 1027-1031. (PubMed)
    • Diepholz, M., Venzke, D., Prinz, S., Batisse, C., Flörchinger, B., Rössle, M., Svergun, D.I., Böttcher, B. and Féthière , J. (2008) A different conformation for the EGC stator sub-complex in solution and in the assembled yeast V-ATPase. Structure, Dec 10;16(12):1789-98. (PubMed)
    • R. Pérez de Diego, M Ortiz-Lombardía, J. Bravo. Crystallization and preliminary X-ray diffraction analysis of the beta subunit Yke2 of the Gim complex from Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun. (2008) Jun 1;64(Pt 6):501-3. (PubMed)
    • Chari A, Golas MM, Klingenhäger M, Neuenkirchen N, Sander B, Englbrecht C, Sickmann A, Stark H, Fischer U. (2008) An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. Cell. Oct 31;135(3):497-509. (PubMed)
    • Akiva, E., Itzhaki, Z. and Margalit, H. (2008) Built-in Loops Allow Versatility in Domain-domain Interactions: Lessons From Self-interacting Domains. Proc. Natl. Acad. Sci. USA 105:13292-13297. (PubMed)
    • Russell RB, Aloy P. (2008) Targeting & tinkering with interaction networks. Nature Biotechnology. Nat Chem Biol. 2008 Nov;4(11):666-73. Review. (PubMed)
    • Roland A Pache and Patrick Aloy (2008) “Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits”, Proteomics, 8: 1959-64 (PubMed)
    • Bahadur RP, Janin J. (2008) Residue conservation in viral capsid assembly. Proteins 71, 407-414. (PubMed)
    • Bahadur RP, Zacharias M, Janin J (2008) Dissecting protein-RNA recognition sites. Nucleic Acid Res. 36, 2705-16. (PubMed)
    • 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.