We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozenhydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ.axoneme ͉ dynein ͉ microtubule ͉ motility ͉ sperm E ukaryotic cilia and flagella are highly ordered organelles that are used by a great variety of species and cell types to generate motion. Despite the diversity of their motile functions, the basic architecture of these machines is remarkably conserved (for review, see ref. 1). All such structures are built on an ordered assembly of microtubules known as the axoneme. The most widely distributed form of the axoneme consists of nine outer microtubule doublets (MTDs) and two singlet microtubules (2, 3). The combination of many structural and enzymatic studies with in vitro motility assays and computer-based simulations has laid a framework for our understanding about how flagellar motion is generated. Sliding between pairs of outer MTDs is powered by the dynein ATPases and converted into flagellar bending as a result of constraints imposed on interdoublet sliding by protein cross-links, such as nexin, which lie between adjacent MTDs (for reviews, see refs. 4 and 5). For an axoneme to generate the complex motions typical of beating cilia and flagella, there must be precise control of dynein's action, both around the circumference and along the length of the axoneme.Because of their biological and medical importance and their utility as a model for other forms of microtubule-based motility (6), flagella and cilia have been studied extensively (for reviews, see refs. 3, 5, and 7-9). However, despite the increase in knowledge about isolated components of the axoneme, much remains to be learned about the mechanical and regulatory mechanisms underlying flagellar motion (3, 10). To elucidate the role of all of the players in axoneme motility, one will need a better understanding of the organization of axonemal elements in situ at a resolution that will characterize the structural changes that they undergo during functional cycles.Sea urchin sperm tails are an admirable material for this sort of study because they are built with a classic ''9 ϩ 2'' axoneme, and their beat pattern is mainly planar, greatly simplifying the geometry of their function in compari...