Yeast and vertebrate nuclear pores display significant morphological similarity 
by electron microscopy, but sequence similarity between the respective proteins 
has been more difficult to observe. Herein we have identified a vertebrate 
nucleoporin, Nup93, in both human and Xenopus that has proved to be an 
evolutionarily related homologue of the yeast nucleoporin Nic96p. Polyclonal 
antiserum to human Nup93 detects corresponding proteins in human, rat, and 
Xenopus cells. Immunofluorescence and immunoelectron microscopy localize 
vertebrate Nup93 at the nuclear basket and at or near the nuclear entry to the 
gated channel of the pore. Immunoprecipitation from both mammalian and Xenopus 
cell extracts indicates that a small fraction of Nup93 physically interacts with 
the nucleoporin p62, just as yeast Nic96p interacts with the yeast p62 
homologue. However, a large fraction of vertebrate Nup93 is extracted from pores 
and is also present in Xenopus egg extracts in complex with a newly discovered 
205-kDa protein. Mass spectrometric sequencing of the human 205-kDa protein 
reveals that this protein is encoded by an open reading frame, KIAAO225, present 
in the human database. The putative human nucleoporin of 205 kDa has related 
sequence homologues in Caenorhabditis elegans and Saccharomyces cerevisiae. The 
analyze the role of the Nup93 complex in the pore, nuclei were assembled that 
lack the Nup93 complex after immunodepletion of a Xenopus nuclear reconstitution 
extract. The Nup93-complex-depleted nuclei are clearly defective for correct 
nuclear pore assembly. From these experiments, we conclude that the vertebrate 
and yeast pore have significant homology in their functionally important cores 
and that, with the identification of Nup93 and the 205-kDa protein, we have 
extended the knowledge of the nearest-neighbor interactions of this core in both 
yeast and vertebrates.