The innermost chorionic layer of Drosophila. II. Three-dimensional structure determination of the 90 degrees crystal form by electron microscopy

The innermost chorionic layer (ICL) within egg shells of Drosophila is composed of a family of related, thin three-dimensional crystals that form a continuous sheath encapsulating the egg shell lumen. Junctions formed by interdigitating lattices play a central role in the construction of this macroscopic assembly. The three-dimensional structure of a two-dimensional crystal isolated from the ICL, with a primitive lattice angle delta of 90 degrees, has been determined from a complete tilt series of a negatively contrasted specimen at a resolution of 25 A. Inspection of the three-dimensional transform after data merging revealed that the space group is c222 and this symmetry was employed to generate a three-dimensional structure. The basic structural unit of the ICL is an octamer, described formally as a tetramer of dimers with point group symmetry 222. There are two classes of dimer in the octamer designated alpha and beta. The chorin octamer is composed of two classes of bent dimers, which make intramolecular contacts at the top and bottom of the molecule. The alpha-dimers are curved outwards away from the crystallographic 2-fold axis, while the beta-dimers are curved towards the molecular center. In addition, lattice contacts are formed primarily by beta-chorin dimers at both the top and bottom surfaces of the unit cell. The molecular weight of a chorin octamer determined from the analysis is about 6 X 10(5). The conformation of the chorin octamer determined here suggests that permutations of a basic molecular mechanism may be adequate to explain both the observed lattice polymorphisms of the ICL and the formation of interplate junctions necessary for the assembly of the macroscopic sheath.     

Three-dimensional crystals of CaATPase from sarcoplasmic reticulum. Symmetry and molecular packing.

Structural studies of CaATPase from sarcoplasmic reticulum have so far been restricted to low resolution due to the poor order of two-dimensional crystal forms. However, we report that three-dimensional microcrystals of detergent-solubilized CaATPase diffract to 7.2 A in x-ray powder patterns and may therefore provide an opportunity to study CaATPase structure at higher resolutions. In the present study, we have characterized the symmetry and molecular packing of negatively stained crystals by electron microscopy (em). By altering the detergent-to-lipid ratio, different sized crystals were produced, which adhere to an em grid in different orientations. Thus, we obtained micrographs of three different projections and from these determined unit cell dimensions to be 151 X 51 X 158 A and the three-dimensional space group to be C2 with an angle beta very close to 90 degrees; x-ray powder patterns of hydrated, unstained crystals yielded dimensions of 166 X 58 X 164 A. Micrographs from each of two principal projections were averaged to produce two-dimensional density maps. Based on these maps and on the previously determined low-resolution structure of CaATPase, a packing diagram for these three-dimensional crystals is presented and major intermolecular contacts are proposed.     

Crystallization and preliminary X-ray diffraction studies of pancreatic spasmolytic polypeptide.

Pancreatic spasmolytic polypeptide (PSP) isolated from porcine pancreas has been crystallized by the hanging drop vapour diffusion method. The crystals belong to the space group I222 or I2(1)2(1)2(1) with cell dimensions a = 181.9 A, b = 54.5 A, c = 72.9 A. The crystals diffract to at least 2.5 A resolution and the asymmetric unit contains two molecules (Vm = 3.9 A3/Da) with a solvent content of 68% as determined by density measurements of the crystals. The self-rotation function suggests that the two molecules within the asymmetric unit are related by a 2-fold axis at either 30 degrees or 60 degrees from a in a plane perpendicular to the b axis.     

Electron microscopic studies on microcrystals of D-ribulose-1,5-biphosphate carboxylase from Dasycladus clavaeformis roth (Ag.)

Crystals of D-ribulose-1,5-biphosphate carboxylase (E.C. 4.1.1.39), naturally occurring in the extraplasmatic space of the unicellular green algae $\text{Dasycladus clavaeformis}$ (Dasycladaceae), were studied by means of electron microscopy and optical diffraction. Optical diffraction patterns were obtained from thin sections. It is shown that the crystals are composed of cubic unit cells with α ～ 31.5 nm. The density of the crystals was estimated as 1.07 ± 0.005 g/ml, a value that gives evidence of the presence of 12 enzyme molecules per unit cell. Optical diffraction studies of the thin sectioned crystals revealed 4mm -symmetry with four 2-fold rotation axes, resulting in at least a 222-symmetry.     

Purification, crystallization and preliminary crystallographic analysis of porcine aldose reductase

Large crystals of porcine aldose reductase have been grown from polyethylene glycol solutions. The crystals are triclinic, space-group P1, with a = 81.3 A, b = 85.9 A, c = 56.6 A, alpha = 102.3 degrees, beta = 103.3 degrees and gamma = 79.0 degrees. The crystals grow within ten days to dimensions of 0.6 mm x 0.4 mm x 0.2 mm and diffract to at least 2.5 A. There are four molecules in the unit cell related by a set of three mutually perpendicular non-crystallographic 2-fold axes.     

P.versicolor龙虾D-甘油醛-3-磷酸脱氢酶的X射线晶体学研究——分子置换法结构测定

由P.versicolor龙虾尾肌提取的HOIO-D-甘油醛-3-磷酸脱氢酶(GAPDH),已长出可供Χ射线衍射用的晶体。初步Χ射线晶体学研究确定:此酶晶体属於C2空间群,不对称单位内含有半个分子,分子坐落在二重轴上。以Homarus Amercanus龙虾GAPDH结构为模型结构,应用分子置换技术进行了低分辨率Χ射线结构分析,结果表明:分子内亚基排列具有222对称性,分子Q轴平行于晶体学二重轴b,分子P和R轴分别平行于晶体学a和c轴。按分子置换法推出的结构模型算得5A分辨率的晶体学R因子为0.46。并获得了一套5A。分辨率的电子密度图。此酶的几种同晶型晶体,特别是荧光NAD衍生物晶体的较高分辨率的结构分析工作正在进行中。     

Three-dimensional reconstruction of innermost chorion layer of Drosophila grimshawi and Drosophila melanogaster eggshell mutant fs(1)384.

A low-resolution three-dimensional structure of the crystalline innermost chorionic layer (ICL) of the Hawaiian species Drosophila grimshawi and the Drosophila melanogaster eggshell mutant fs(1)384 has been calculated from electron microscope images of tilted negatively stained specimens. The isolated ICL of Drosophila grimshawi is a three-layer structure, about 36 nm thick, whereas the ICL of Drosophila melanogaster eggshell mutant fs(1)384 is a single layer, about 12 nm thick. Each unit in both crystalline structures includes octamers made up of four heterodimers. Crosslinks between the structural elements, both within and between unit cells form an interconnecting network, apparently important in maintaining the integrity of the layer. A model which may account for the ICL self-assembly formation in vivo and the ICL observed lattice polymorphism is proposed, combining data from the three-dimensional reconstruction work and secondary structure features of the ICL component proteins s36 and s38.     

Mass Determination of the Unit Cell of the Innermost Chorionic Layer in Drosophilidae by Scanning Transmission Electron Microscopy

The innermost chorionic layer (ICL) in eggshells of Drosophila melanogaster is a naturally occurring patchwork of thin three-dimensional crystalline plates located between the inner endochorion and the vitelline envelope. The mass-per-unit area of the ICL has been measured from scanning transmission electron microscope images of isolated unstained material and it was possible to distinguish up to four layers with the majority of the crystalline sheets being one to three layers thick. Taking into account the unit cell areas for the different crystals, we have estimated the mean ICL subunit sizes to be 36 kDa for Drosophila melanogaster, 35 kDa for Drosophila auraria, and 33 kDa for Drosophila teissieri. The results suggest that the three different Drosophilidae species have very similar average subunit masses.     

Three-dimensional architecture of the cell sheath and septa of Methanospirillum hungatei.

The methanogenic bacterium Methanospirillum hungatei exists as filaments which have a very unusual cell wall architecture, comprising a long cylindrical sheath within which there may be many individual cells arranged in a line. The sheath has a two-dimensional crystalline structure, and the cells are separated within the tube by septa which also have a crystalline structure. We have used computer image processing of tilted-view electron micrographs to analyze the structure in negative stains of both of these components in three dimensions. The repeating unit of the sheath consists of four approximately spherical domains ca. 2.5 nm in diameter arranged in a row. Based on observations of the type of lattice imperfections that occur, we suggest that each of the domains represents a separate polypeptide subunit and that the subunits are incorporated into the wall one by one. The septa are circular plates of remarkably constant size. They are normally found as double layers. They are hexagonally symmetrical and consist of trimerically associated subunits which interact about dimer axes to form an open network containing large pores ca. 15 nm in diameter.     

Three-dimensional reconstruction of innermost chorion layer from Drosophila melanogaster

A low-resolution three-dimensional structure of the crystalline innermost chorion layer (ICL) has been calculated from electron microscope images of tilted negatively stained crystals. The isolated ICL is a single layer, about 12 nm thick and appears to be made up of two types of subunits, each approximately 3 nm in diameter, arranged regularly as groups of four heterodimers in space group C222. Linking density between these groups of subunits, maintaining the integrity of the layer, appears to be confined mainly to the outer surfaces of the ICL.     

Three-dimensional reconstruction of innermost chorion layer from Drosophila melanogaster

A low-resolution three-dimensional structure of the crystalline innermost chorion layer (ICL) has been calculated from electron microscope images of tilted negatively stained crystals. The isolated ICL is a single layer, about 12 nm thick and appears to be made up of two types of subunits, each approximately 3 nm in diameter, arranged regularly as groups of four heterodimers in space group C222. Linking density between these groups of subunits, maintaining the integrity of the layer, appears to be confined mainly to the outer surfaces of the ICL.     

Crystallization and preliminary X-ray analysis of complexes of peptide inhibitors with human recombinant and mouse submandibular renins.

Inhibitor-complexed crystals of mouse and human renins suitable for X-ray analysis have been prepared. The mouse renin is complexed with a non-hydrolysable decapeptide analogue of rat angiotensinogen containing a hydroxyethylene isostere in place of the scissile bond. The crystals are monoclinic, space group P2(1) with cell dimensions a = 78.3 A, b = 117.8 A, c = 85.9 A, beta = 101.18 degrees containing four molecules per asymmetric unit. The human renin is fully glycosylated and complexed with a tetrapeptide containing norstatine. The complex crystallises in the cubic space group P2(1)3 with a = 143.1 A and has two molecules in the asymmetric unit. The rotation function of the mouse renin complex indicates pseudo 222 symmetry while that of human renin indicates a pseudo 2-fold axis. Full structural analyses of the two complexes are underway.     

Arrangement of subunits in peanut lectin. Rotation function and chemical cross-linking studies

X-ray intensity data from the native orthorhombic crystals of peanut lectin have been collected using oscillation photography. Rotation function studies using data up to a resolution of 4.5 A indicate that the four subunits in the molecule, which constitute the asymmetric unit in the crystals, are related to one another by three mutually perpendicular noncrystallographic 2-fold axes. Chemical cross-linking experiments in solution followed by sodium dodecyl sulfate gel electrophoresis, carried out in parallel, suggest that there is more than one type of intersubunit approach in the molecule. Rotation function and cross-linking studies thus show that the tetrameric molecule of peanut lectin is a dimer of a dimer. The two monomers in a dimer are related by a 2-fold axis. The two dimers are in turn related by another 2-fold axis perpendicular to the one that relates the two monomers in the dimer, endowing the molecule with 222 (D2) symmetry.     

Crystallization and preliminary x-ray diffraction study of the flavoprotein NADH peroxidase from Streptococcus faecalis 10C1

NADH peroxidase from Streptococcus faecalis 10C1 has been crystallized from ammonium sulfate solutions using the hanging drop vapor diffusion method. Depending on pH, the crystals grew in the orthorhombic space group I222 or one of its subgroups P222 or P2(1)2(1)2 (or one of its two permutations). In both cases the unit cell axes are a = 76.6 A, b = 132.9 A, and c = 145.7 A. There are two monomers/asymmetric unit in the body-centered crystal form and four in the primitive one. The enzyme is catalytically active in the crystalline state. The crystals diffract to at least 2.5 A resolution; they are stable in the x-ray beam and hence suitable for detailed three-dimensional structure determination.     

Electron microscopy of thin-sectioned three-dimensional crystals of SecA protein from Escherichia coli: structure in projection at 40 A resolution.

SecA is a single-chain, membrane-associated polypeptide (102 kDa) which functions as an essential component of the protein export machinery of Escherichia coli. SecA has been crystallized from ammonium sulfate as small, three-dimensional bipyramidal crystals (0.1 x 0.1 x 0.05 mm). These crystals did not demonstrate detectable diffraction of X-rays from rotating anode sources. For study by electron microscopy, individual crystals were cross-linked in glutaraldehyde and OsO4 solutions, dehydrated, embedded in epoxy resin, and sectioned normal to crystallographic axial directions inferred from the external morphology of the crystals. Fourier transformation of processed images of untilted thin sections stained with uranyl acetate and lead citrate show reflections extending to 31 A resolution. Diffraction data and reconstructed images of the projected density of the unit cell contents indicate that the bipyramidal SecA crystals belong to orthorhombic space group C222(1) with unit cell dimensions a = 414 A, b = 381 A, and c = 243 A. Filtered images and density maps of mutually orthogonal projections of the unit cell contents are consistent with a three-dimensional model in which the asymmetric unit contains eight SecA monomers. The large unit cell dimensions and packing of protein monomers suggest that SecA is crystallizing as an oligomer of either dimers or tetramers.     

Crystallization and preliminary X-ray analysis of human angiogenin.

Crystals of recombinant human angiogenin have been grown from solutions containing sodium potassium tartrate and polyethylene glycol as precipitants. They belong to the space group C222(1) (a = 83.36 A, b = 120.64 A, c = 37.72 A) and contain a single molecule in the asymmetric unit. The crystals diffract to at least 2.3 A resolution and are suitable for three-dimensional X-ray structural analysis.     

Preliminary crystallographic data for stearoyl-acyl carrier protein desaturase from castor seed.

Recombinant stearoyl-acyl carrier protein desaturase (EC 1.14.99.6) from castor seed has been crystallized with polyethylene glycol 8000 as precipitant. The crystals are orthorhombic, space group P2(1)2(1)2(1) with cell dimensions a = 81.3, b = 146.4 and c = 197.7 A. The observed diffraction pattern extends to at least 2.5 A resolution. Rotation function calculations indicate a non-crystallographic 3-fold rotation axis parallel to the crystallographic a-axis. Perpendicular to this axis, 2-fold rotation axes were found at 30 degrees intervals, i.e. maxima at kappa = 180 degrees, phi = 90 degrees and omega = 30 degrees and 60 degrees, respectively. Together with the packing density of the crystals (Vm = 2.4 A3/Da for n = 6), these results suggest, that the crystal asymmetric unit most likely contains a hexamer of desaturase subunits.     

Crystallization of bacteriorhodopsin from bicelle formulations at room temperature

We showed previously that high-quality crystals of bacteriorhodopsin (bR) from Halobacterium salinarum can be obtained from bicelle-forming DMPC/CHAPSO mixtures at 37 degrees C. As many membrane proteins are not sufficiently stable for crystallization at this high temperature, we tested whether the bicelle method could be applied at a lower temperature. Here we show that bR can be crystallized at room temperature using two different bicelle-forming compositions: DMPC/CHAPSO and DTPC/CHAPSO. The DTPC/CHAPSO crystals grown at room temperature are essentially identical to the previous, twinned crystals: space group P21 with unit cell dimensions of a = 44.7 A, b = 108.7 A, c = 55.8 A, beta = 113.6 degrees . The room-temperature DMPC/CHAPSO crystals are untwinned, however, and belong to space group C222(1) with the following unit cell dimensions: a = 44.7 A, b = 102.5 A, c = 128.2 A. The bR protein packs into almost identical layers in the two crystal forms, but the layers stack differently. The new untwinned crystal form yielded clear density for a previously unresolved CHAPSO molecule inserted between protein subunits within the layers. The ability to grow crystals at room temperature significantly expands the applicability of bicelle crystallization.     

Two-dimensional crystallization of Ca-ATPase by detergent removal.

By using Bio-Beads as a detergent-removing agent, it has been possible to produce detergent-depleted two-dimensional crystals of purified Ca-ATPase. The crystallinity and morphology of these different crystals were analyzed by electron microscopy under different experimental conditions. A lipid-to-protein ratio below 0.4 w/w was required for crystal formation. The rate of detergent removal critically affected crystal morphology, and large multilamellar crystalline sheets or wide unilamellar tubes were generated upon slow or fast detergent removal, respectively. Electron crystallographic analysis indicated unit cell parameters of a = 159 A, b = 54 A, and gamma = 90 degrees for both types of crystals, and projection maps at 15-A resolution were consistent with Ca-ATPase molecules alternately facing the two sides of the membrane. Crystal formation was also affected by the protein conformation. Indeed, tubular and multilamellar crystals both required the presence of Ca2+; the presence of ADP gave rise to another type of packing within the unit cell (a = 86 A, b = 77 A, and gamma = 90 degrees), while maintaining a bipolar orientation of the molecules within the bilayer. All of the results are discussed in terms of nucleation and crystal growth, and a model of crystallogenesis is proposed that may be generally true for asymmetrical proteins with a large hydrophilic cytoplasmic domain.     

Beta-bungarotoxin. Preparation and characterization of crystals suitable for structural analysis

Phospholipases in some snake venoms are potent neurotoxins that target their enzymatic action to the synaptic membrane. One of these is the heterodimeric neurotoxin, beta-bungarotoxin, which binds with a protease inhibitor-like subunit to a presynaptic potassium channel and then blocks neurotransmission with a second subunit that has phospholipase A2 activity. We have prepared and characterized well ordered crystals of the most toxic beta-bungarotoxin isoform, beta 1-bungarotoxin. The crystals are monoclinic, space group C2, with unit cell parameters: a = 176.5 A, b = 39.3 A, c = 92.7 A, and beta = 114.8 degrees. Rotation-function analysis of the Patterson function, as calculated from a 2.3-A data set, reveals an asymmetric unit composed of four heterodimers. These heterodimers appear to be associated as two crystallographically distinct (AB)4 tetramers, each having dihedral D2 symmetry. The two are positioned with equivalent molecular 2-fold axes coincident with crystallographic dyads, but rotated by 55 degrees relative to one another. X-ray analysis of these crystals will permit direct visualization of the specific structural motifs and chemical features that underlie phospholipase neurotoxicity.