Structure of light-harvesting chlorophyll a/b protein complex from plant photosynthetic membranes at 7 A resolution...

The structure of thin three-dimensional crystals of the light-harvesting chlorophyll a/b protein complex, an integral membrane protein from the photosynthetic membrane of chloroplasts, has been determined at 7 A (1 A = 0.1 nm) resolution in projection. The structure analysis was carried out by image processing of low-dose electron micrographs, and electron diffraction of thin three-dimensional crystals preserved in tannin. The three-dimensional crystals appeared to be stacks of two-dimensional crystals having p321 symmetry. Results of the image analysis indicated that the crystals were disordered, due to random translational displacement of stacked layers. This was established by a translation search routine that used the low-resolution projection of a single layer as a reference. The reference map was derived from the symmetrized average of two images that showed features consistent with the projected structure of negatively stained two-dimensional crystals. The phase shift resulting from the displacement of each layer was corrected. Phase shifts were then refined by minimizing the phase residual, bringing all layers to the same phase origin. Refined phases from different images were in agreement and reliable to 7 A resolution. A projection map was generated from the averaged phases and electron diffraction amplitudes. The map showed that the complex was a trimer composed of three protein monomers related by 3-fold symmetry. The projected density within the protein monomer suggested membrane-spanning alpha-helices roughly perpendicular to the crystal plane. The density in the centre and on the periphery of the trimeric complex was lower than that of the protein, indicating that this region contained low-density matter, such as lipids and antenna chlorophylls.