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The three-dimensional structure of tumor necrosis factor (TNF-alpha), a protein
hormone secreted by macrophages, has been determined at 2.6 A resolution by
x-ray crystallography. Phases were determined by multiple isomorphous
replacement using data collected from five heavy atom derivatives. The multiple
isomorphous replacement phases were further improved by real space symmetry
averaging, exploiting the noncrystallographic 3-fold symmetry of the TNF-alpha
trimer. An atomic model corresponding to the known amino acid sequence of
TNF-alpha was readily built into the electron density map calculated with these
improved phases. The 17,350-dalton monomer forms an elongated, antiparallel
beta-pleated sheet sandwich with a "jelly-roll" topology. Three monomers
associate intimately about a 3-fold axis of symmetry to form a compact
bell-shaped trimer. Examination of the model and comparison to known protein
structures reveals striking structural homology to several viral coat proteins,
particularly satellite tobacco necrosis virus. Locations of residues conserved
between TNF-alpha and lymphotoxin (TNF-beta, a related cytokine known to bind to
the same receptors as TNF-alpha) suggest that lymphotoxin, like TNF-alpha, binds
to the receptor as a trimer and that the general site of interaction with the
receptor is at the "base" of the trimer.
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