Differential Arrangements of Conserved Building Blocks among Homologs of the Rad50/Mre11 DNA Repair Protein Complex Martijn de Jager 1 , Kelly M. Trujillo 2 , Patrick Sung 3 , Karl-Peter Hopfner 4 James P. Carney 5 , John A. Tainer 6 , John C. Connelly 7 David R. F. Leach 7 , Roland Kanaar 1,8 and Claire Wyman 1,8 * 1 Department of Cell Biology and Genetics, Erasmus MC, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands 2 Stowers Institute for Medical Research, 1000 E. 50th Street Kansas City, MO 64110, USA 3 Yale University School of Medicine, Molecular Biophysics and Biochemistry, 333 Cedar Street, New Haven, CT 06520 USA 4 Gene Center and Institute of Biochemistry, University of Munich, Feodor-Lynen-Strasse 25 81377 Munich, Germany 5 The Radiation Oncology Research Laboratory and the Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore MD 21201, USA 6 Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037 USA 7 Institute of Cell and Molecular Biology, University of Edinburgh Kings Buildings, Edinburgh EH9 3JR, UK 8 Department of Radiation Oncology, Erasmus MC Daniel 3000 DR Rotterdam, The Netherlands Structural maintenance of chromosomes (SMC) proteins have diverse cellular functions including chromosome segregation, condensation and DNA repair. They are grouped based on a conserved set of distinct struc- tural motifs. All SMC proteins are predicted to have a bipartite ATPase domain that is separated by a long region predicted to form a coiled coil. Recent structural data on a variety of SMC proteins shows them to be arranged as long intramolecular coiled coils with a globular ATPase at one end. SMC proteins function in pairs as heterodimers or as homo- dimers often in complexes with other proteins. We expect the arrange- ment of the SMC protein domains in complex assemblies to have important implications for their diverse functions. We used scanning force microscopy imaging to determine the architecture of human, Saccharomyces cerevisiae, and Pyrococcus furiosus Rad50/Mre11, Escherichia coli SbcCD, and S. cerevisiae SMC1/SMC3 cohesin SMC complexes. Two distinct architectural arrangements are described, based on the way their components were connected. The eukaryotic complexes were similar to each other and differed from their prokaryotic and archaeal homologs. These similarities and differences are discussed with respect to their diverse mechanistic roles in chromosome metabolism. q 2004 Elsevier Ltd. All rights reserved. Keywords: scanning force microscopy (SFM); structural maintenance of chromosomes (SMC); protein architecture; DNA metabolism; SbcCD *Corresponding author 0022-2836/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. E-mail address of the corresponding author: c.wyman@erasmusmc.nl Abbreviations used: SMC, structural maintenance of chromosomes; SFM, scanning force microscopy. doi:10.1016/j.jmb.2004.04.014 J. Mol. Biol. (2004) 339, 937–949