Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy

Routine single particle CryoEM sample and grid characterization by tomography

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.

The cryo-EM structure of gastric H+,K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitors

The gastric proton pump H⁺,K⁺-ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K⁺-competitive acid blockers (P-CABs), have potential application as acid-suppressing drugs. We determined the electron crystallographic structure of H⁺,K⁺-ATPase at 6.5 Å resolution in the E2P state with bound BYK99, a potent P-CAB with a restricted ring structure. The BYK99 bound structure has an almost identical profile to that of a previously determined structure with bound SCH28080, the original P-CAB prototype, but is significantly different from the previously reported P-CAB-free form, illustrating a common conformational change is required for P-CAB binding. The shared conformational changes include a distinct movement of transmembrane helix 2 (M2), from its position in the previously reported P-CAB-free form, to a location proximal to the P-CAB binding site in the present BYK99-bound structure. Site-specific mutagenesis within M2 revealed that D137 and N138, which face the P-CAB binding site in our model, significantly affect the inhibition constant (K_i) of P-CABs. We also found that A335 is likely to be near the bridging nitrogen at the restricted ring structure of the BYK99 inhibitor. These provide clues to elucidate the binding site parameters and mechanism of P-CAB inhibition of gastric acid secretion.

Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes

Mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. Direct structural evidence on the transient cytochrome c oxidase–cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. Here, we report on the 2D crystallization of monomeric bovine cytochrome c oxidase with tightly bound cytochrome c at a molar ratio of 1:1 in reconstituted lipid membranes at the basic pH of 8.5 and low ionic strength.

Two-Dimensional Crystallization of Gastric H(+),K(+)-ATPase for Structural Analysis by Electron Crystallography

Electron crystallography of two-dimensional (2D) crystals has provided important information on the structural biology of P-type ATPases. Here, I describe the procedure for making 2D crystals of gastric H(+),K(+)-ATPase purified from pig stomach. The 2D crystals are produced by dialyzing detergent-solubilized H(+),K(+)-ATPase mixed with synthetic phospholipids. Removal of the detergent induces the reconstitution of H(+),K(+)-ATPase molecules into the lipid bilayer. In the presence of fluorinated phosphate analogs, or in combination with transporting cations or the specific antagonist SCH28080, H(+),K(+)-ATPase forms crystalline 2D arrays. The molecular conformation and morphology of the 2D crystals vary depending on the crystallizing conditions. Using these 2D crystals, three-dimensional structures of H(+),K(+)-ATPase can be generated by data correction from ice-embedded 2D crystals using cryo-electron microscopy, followed by processing the recorded images using electron crystallography methods.

Systematic comparison of molecular conformations of H+,K+-ATPase reveals an important contribution of the A-M2 linker for the luminal gating

Gastric H⁺,K⁺-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K⁺-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H⁺,K⁺-ATPase is consistent with that observed in sarcoplasmic reticulum Ca²⁺-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general.

Three-dimensional structure of bovine heart NADH: ubiquinone oxidoreductase (complex I) by electron microscopy of a single negatively stained two-dimensional crystal

Bovine heart NADH:ubiquinone oxidoreductase (complex I), which is the largest (about 1 MDa) membrane protein complex in the mitochondrial respiratory chain, catalyzes the electron transfer from NADH to ubiquinone, coupled with proton pumping. We have crystallized bovine complex I in reconstituted lipid bilayers and obtained a three-dimensional density map by the electron crystallographic analysis of a single negatively stained two-dimensional crystal. The asymmetric unit with dimensions of a = 388 Å, b = 129 Å and γ = 90° contains two molecules and is of P1 symmetry. Structural differences between the two molecules indicate flexibility of the hydrophilic domain relative to the membrane-embedded domain.

Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondria

Mitochondrial F-ATP synthase produces the majority of ATP for cellular functions requiring free energy. The structural basis for proton motive force-driven rotational catalysis of ATP formation in the holoenzyme remains to be determined. Here, the purification and two-dimensional crystallization of bovine heart mitochondrial F-ATP synthase are reported. Two-dimensional crystals of up to 1 µm in size were grown by dialysis-mediated detergent removal from a mixture of decylmaltoside-solubilized 1,2-dimyristoyl-sn-glycero-3-phosphocholine and F-ATP synthase against a detergent-free buffer. A projection map calculated from an electron micrograph of a negatively stained two-dimensional crystal revealed unit-cell parameters of a = 185.0, b = 170.3 Å, γ = 92.5°.