An electron-density map of the mouse galactan-binding immunoglobulin 1539 (IgA2,K) Fab has been calculated to a resolution of 4.5 A by the method of heavy atom isomorphous replacement with four derivatives. The map has been interpreted with the aid of a com uter program which systematically searched for the best fit between the electrondensity map and the known coordinates of individual immunoglobulin domains. The quaternary structure of J539 Fab at this resolution appears similar to that of another mouse immunoglobulin, IgA2,K Fab, McPC603. The model coordinates for J539 Fab should allow us to proceed directly to a high-resolution structure determination without further heavy atom isomorphous replacement.The crystal structures of three immunoglobulin Fabs have been reported (1-3). One of these, the mouse myeloma protein McPC603, belongs to a class of immunoglobulins that bind specifically to phosphocholine. In this paper, we present the results of.a structural analysis at 4.5-A resolution of a second mouse Fab, the galactan-binding immunoglobulin J539. A molecular model has been constructed with the aid of a computer search procedure used previously in the interpretation of the electron-density map of an intact immunoglobulin (4). The model allows us to describe the quaternary structural interactions between the constituent domains and domain pairs of the J539 Fab and reveals a general similarity to McPC603.
MATERIALS AND METHODSThe immunoglobulin J539 [a mouse IgA2,K; anti-(1-',6)-/-D-galactan] was isolated and purified as described (5), and pepsin fragments were obtained by using a published procedure (6). Useful heavy atom derivatives were obtained by soaking J539 Fab crystals in stabilizing solutions with 0.25 mM K2Pt(CNS)6 for 2 weeks, 1 mM K2PtCl4 for 1 week, 0.3 mM K2HgI4 for 2 weeks, and 50 mM KI/1 mM chloramine-T (Eastman Kodak) for 1 week. The iodine-derivatized crystals were washed with fresh stabilizing solution after the soaking period. Unique sets of three-dimensional reflection data to 4.5-A spacings were collected from native and derivative crystals with a Picker FACS-1 diffractometer operated in the T-scan mode and using Cu Ka radiation. The various data sets were placed on the same relative scale, and pseudo temperature factors were applied to correct for differences in intensity fall-off. The K2Pt(CNS)6 derivative was analyzed first, and difference Patterson maps, readily interpretable, revealed one site of substitution (Fig. 1). After preliminary refinement with projection data only, the coordinates and occupancy of the K2Pt(CNS)6 site were used to determine the signs of the centric native protein reflections. These signs were used to examine the K2PtCI4 and K2HgI4 derivatives by difference Fourier analysis. The variables for these three heavy atom derivatives were then subjected to alternating cycles of least squares refinement and phase determination with the three-dimensional data. The resulting phasesThe publication costs of this article were defrayed in part by page charge paym...