The structure of a naturally occurring variant of human granulocyte-macrophage colony-stimulating factor

Human Granulocyte-Macrophage Colony-Stimulating Factor (hGM-CSF) is a glycoprotein (14-35 kD) that stimulates the growth and activity of white blood cells. The three-dimensional structure of a non-glycosylated recombinant form of hGM-CSF has been determined (K. Diederichs et al. (Science 254, 1779(1991)) and Walter et al. (J.M.B. 224, 1075(1992))). hGM-CSF is a four $\alpha$-helical bundle with up-up-down-down connectivity and an uncommon threaded loop topology. Here the structure of a naturally occurring variant of hGM-CSF (I80-hGM-CSF) which differs from the previously reported structures (M80-hGM-CSF) by one amino acid with Ile instead of Met at position 80 is described. I80-hGM-CSF crystals from 2.2 M NaH$\sb2$PO$\sb4$/K$\sb2$HPO$\sb4$, space group ${\rm P}2\sb12\sb12\sb1,$ two molecules per asymmetric unit, cell dimensions of a = 46.27 b = 58.77 c = 125.77 A were flash cooled to 137 K and data were measured to a resolution limit of 2.8 A. The structure was refined by simulated annealing using coordinates for M80-hGM-CSF generously provided by P. A. Karplus (K. Diederichs et al., Science 254, 1779(1991)) with a reduction in the R-factor from 37.9% to 20.87%. The r.m.s. deviation between the two structures is 1.33, 0.912, and 1.643 A for all non-hydrogen, main-chain and side-chain atoms, respectively. Ile 80 is located in the interior of the molecule and adopts a conformation similar to Met 80 in the M80-hGM-CSF structure; the packing of surrounding residues is not significantly changed. Approximately 25% of the residues in the I80-hGM-CSF structure have disordered side-chain conformations. Significant main-chain differences are observed between the two structures and occur in eight regions (residues 4-6, 25-32, 34-38, 45-55, 64-70, 92-98, 116-117, 122-124) that are associated with high B-factors in both structures. The largest differences occur at the amino-terminus (4-6) and in the threaded loop region (45-55). These differences observed between the I80- and M80-hGM-CSF structures reflect the inherent mobility in certain regions of its polypeptide chain