The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase - PubMed (original) (raw)

The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase

T S Baker et al. J Mol Biol. 1975.

Abstract

Single crystals of d-ribulose-1,5-diphosphate carboxylase from tobacco leaves, Nicotiana tabacum (variety Turkish Samsun), have been examined by X-ray diffraction, electron microscopy, and optical diffraction. Twelve molecules are loosely packed into a body-centered cubic unit cell, space group 14132 with cell dimension a = 383 Å. The asymmetric unit is one quarter of a molecule, and the minimum molecular symmetry is 222. This symmetry when combined with estimates of the two subunit masses and stoichiometry is compatible with a molecular structure of the composition L8S8 (L is large subunit, S is small). If all bonds between large and small subunits are equivalent, the true molecular symmetry is 422; this symmetry is consistent with molecular images in micrographs.

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Figures

PLATE I

(a) A field of RuDPCase molecules negatively stained with uranyl acetate. Magnification 250,000 ×. (b) to (i) Enlarged images of molecules displaying a central hole. This orientation may correspond to a view parallel to a unique 4-fold axis of molecular symmetry. Magnification 750,000 ×. (j) and (k) Enlarged images displaying a central line of stain through the molecules.

PLATE II

(a) and (b) Fragments of form I RuDPCase crystals, negatively stained in uranyl acetate. Magnification 200,000 ×. (c) Drawing illustrating the packing of 12 molecules per unit cell in space group 14132. The drawing represents a projection of the magnified (200,000 ×) crystal structure viewed along the crystallographic axis (perpendicular to the 100 crystallographic planes). Molecules are depicted as white circles, 120 Å in diameter, to correspond with images of negatively stained individual molecules. The black areas represent the presence of heavy met.al contrasting agent (uranyl acetate). Four unit cells are outlined in the lower right-hand corner. An enlarged view of the molecular packing at a magnification of 400,000 × is drawn in tho upper right-hand corner ; individual molecules are outlined in black to reveal the spatial arrangement of molecules in the special positions within the crystal. (d) A drawing similar to (c), representing a view perpendicular to the 100 crystallographic planes of space group 1432 with 12 molecules per unit cell. Note the similarity of (a) and (b) to (c), and dissimilarity to (d).

PLATE III

(a) to (c) Drawings of a rhombic dodecaherdral crystal viewed parallel to the 2, 3, and 4-fold axes, respectively. The crystal depicted in (a) is rotated 90° about the 2-fold axis with respect to the diffraction pattern to its right. The orientation of the crystal drawn in (b) is identical with the orientation of the sections and diffraction pattern3 in (d), (f), (h), (j), and (m). The crystal in (c) is rotated 45° with respect to the (e), (g), (i), (k), and (n). (d) and (e) Projection drawings representing magnified (112,000 ×) images of the molecular packing in space group 14132 viewed perpendicular to the 111 and 100 crystal planes. Molecules are colored black to correspond with electron microgmphs of positively stained thin sections of embedded crystals appearing in (f) and (g). The drawings depict projections of the structure thicker than one unit cell. (f) and (g) Electron micrographs of positively stained thin sections of fixed, dehydrated, and embedded form I RuDPCase crystals at a magnification of 112,000 × . Sections are perpendicular to the 3 and 4-fold axes of the crystal and are therefore views of the III and 100 crystallographic planes. (h) and (i) Optica1 diffraction patterns of the drawings in (d) and (o) reproduced at the same scale as the X-ray precession photographs in (m) and (n). (j) and (k) Optical diffraction patterns of the electron micrographs in (f) and (g). The patterns are enlarged four times larger than the scale of the diffraction patterns in (h) and (i) and (m) and (n). (I) to (n) Three-degree zero-level precession photographs taken with the precession axis parallel to Lhe 2, 3, and 4-fold crystal axes. The central portion of each pattern is hidden hy the shadow of the lead beam stop . An image of the focused X-ray beam appears in the center of each pattern and defines t he position of the 0,0,0 reflection. The diffraction patterns have been magnified 4·5 times from the original photographs.

PLATE III

PLATE IV

Projection drawings of sections of various thicknesses from the unit cell of a form I crystal. All views are perpendicular to the 111 crystal planes, and are at a magnification of 150,000 ×. Molecules are shown black, to represent positive staining; solvent is white. In the upper left-hand corner, a rhombic dodecahedral crystal is shown with a view parallel to its 3-fold axis. In the upper right-hand corner is shown an electron micrograph of a positively stained section of thickness less than one unit cell. Note the similarities to the drawings for thicknesses of 90 to 255 Å.

PLATE V

Micrograph of crystal sections showing folds produced during transfer of the sections onto electron microscope grids. (a) A measure of the fold thickness (310 Å) enables one to estimate the section thiclmess (155 Å); (sec Small, 1968). Our interpretation, that this feature is indeed a double fold, is supported by a central line in the original negative. This proves it is possible to cut sections as thin as those illustrated in Plate IV. Magnification 180,000 ×. Inset magnification 36,000 ×. (b) A second folded section; the double thickness (575 Å) suggests the section thiclmess is 288 Å Note the central line in the fold. Magnification 180,000 ×. Inset magnification 47,000 ×.

PLATE V

References

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The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase - PubMed (original) (raw)