Complex I is the largest complex in the respiratory chain, and the least understood. We have determined the 3D structure of complex 1 from Yarrowia lipolytica lacking the flavoprotein part of the N-module, which consists of the 51 kDa (NUBM) and the 24 kDa (NUHM) subunits. The reconstruction was determined by 3D electron microscopy of single particles. A comparison to our earlier reconstruction of the complete Y lipolitica complex 1 clearly assigns the two flavoprotein subunits to an outer lobe of the peripheral arm of complex 1. Localizing the two subunits allowed us to fit the X-ray structure of the hydrophilic fragment of complex 1 from Thermus thermophilus. The fit that is most consistent with previous immuno-electron microscopic data predicts that the ubiquinone reducing catalytic center resides in the second peripheral lobe, while the 75 kDa subunit is placed near the previously seen connection between the peripheral arm and the membrane arm protrusions. (c) 2007 Elsevier Inc. All rights reserved.