The mitochondrial outer membrane contains numerous copies of a channel protein, VDAC, that is thought to be the main permeability pathway through this membrane for polar molecules and ions. Low-dose electron microscopy has been used to obtain images of two-dimensional crystals of this channel. (produced by treating outer membranes from fungal mitochondria with phospholipase A(2)) embedded in vitreous ice or aurothioglucose. The angular orientation of the channels in the unit cell of one type of array has been determined by rotational correlation analysis. The location of the amino-terminal segment of the protein (which, according to circular dichroism, forms an alpha-helix in nonpolar solvents and detergent solutions) has been determined by labeling arrays with Fab prepared from antibodies directed against residues 1-20. The three-dimensional structure of the channel has been obtained by applying Fourier reconstruction methods to projections of tilted crystals embedded in aurothioglucose, followed by averaging of the three non-symmetry-related channels in the unit cell. The results of this study indicate that the wall of VDAC's lumen has several irregular features (uneven height, grooves) and that the aminoterminal segment extends away from the lumen in this crystalline state. (C) 1995 Academic Press, Inc.