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cryo-electron microscopy

Cryo-EM structures of human OAT1 reveal drug binding and inhibition mechanisms.

Fengbin Wang, Yanqui Gu, J. Patrick O'Brien, Sophia M. Yi, Sibel Ebru Yalcin, Vishok Srikanth, Cong Shen, Dennis Vu, Nicole L. Ing, Allon I. Hochbaum, Edward H. Egelman, and Nikhil S. 1ofw. Cell 177:361-9, April 4, 2019. doi:10.1016/j.cell.2019.03.029

Structure Tour

spinqualitylabelsall models Geobacter sulfurreducens outer membrane cytochrome S (OmcS) 6ef8. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Background The electrically conductive nanowires that extend from cells of Geobacter sulfurreducens have long been thought to be pili assembled from PilA protein. However, the evidence was indirect. Here, the structure of filaments of wild type Geobacter sulfurreducens, confirmed to be electrically conductive, was determined by cryo-electron microscopy (6ef8). Surprisingly, these nanowires are assembled from outer membrane cytochrome OmcS. These findings were confirmed a short time later (6nef) by a group expressing alternative interpretations. Nanowire Structure Click the green links below to change the molecular scene. Drag to rotate. Zoom the molecule with your mouse wheel, or Shift-Drag up/down. A nanowire model composed of 7 OmcS protein chains, each shown a different color, was constructed from the 3.2-3.7 Å cryo-EM density (restore initial scene). The filament is ~4 nm in diamater, and has a characteristic undulating or sinusoidal form with a wavelength (pitch) of ~20 nm. The OmcS monomers have 407 amino acids each. The carboxy terminus of each monomer contacts the amino terminus of the next.  Amino Terminus                 Carboxy Terminus  The amino terminus forms a bulge that fits into the slightly concave carboxy-terminal face of the contacting subunit. OmcS Structure The OmcS monomer has remarkably little secondary structure. Alpha Helices, 310 Helices,  Beta Strands ,  Loops . The structure assigned by the authors is 77% loops; Jmol objectively assigns 82% loops. The authors assigned 10% alpha helices, 7% 310 helices, and 6% beta strands. The OmcS structure determined by Filman et al. was very similar, with 80% loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: 1ofw, 3ucp, and 3ov0 had 45%, 49%, and 60% loops respectively. Hemes Each OmcS monomer contains 6 hemes: C O N Fe. The hemes are arranged in parallel-displaced pairs. Each pair is orthogonal to the next pair. The hemes at each monomer-monomer interface form a parallel-displaced pair, which likely contributes to the stability of the filament. More importantly, this produces a continuous chain of hemes through the length of the filament. This continuous chain of hemes is believed to be the basis of the electrical conductivity. Cysteine Anchors Each heme is covalently anchored to two cysteines, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls): C O N S Fe. 12 CxxCH motifs in the OmcS sequence anchor the 6 hemes within each OmcS chain. Histidine to Iron Each heme iron atom is coordinated by two histidine sidechain nitrogens, in addition to the four heme nitrogens. The iron of heme 5 (the next to last heme at the carboxy end of the chain) is bound to His 332 from its own chain (Chain A), and His 16 in the N-terminal "bulge" of the next protein chain (Chain B) in the filament. This inter-chain histidine-iron bond is undoubtedly important in strengthening the monomer-monomer interfaces in the filament. The histidines bound to hemes 1, 2, 3, 4, and 6 are all in the same protein chain that contains those hemes. Salt Bridges Using a 4.0 Å cutoff, 6ef8 has 7 salt bridges between amino acid sidechains (not shown). One of these, Arg176 to Asp432 (2.6 Å) (Chain A, Chain B, O, N), is between protein chains, further strengthening the interfaces between monomers in the filament. (These opposing charges are 4.9 Å apart in 6nef.) The amino-terminal NH3+ on Phe 1 forms a salt bridge with one carboxy of heme 2 (HEC503; 3.65 Å; not shown). Each heme has close to zero net charge, since the two carboxyls are compenated by Fe++. About half of the heme carboxyls are on the surface, exposed to water (not shown). Several of the heme carboxyls form salt bridges with sidechains of arginine or lysine (not shown). Buried Cations The sidechain nitrogens of Arg333, Arg344, and Arg375 are buried. None have anions within 5 Å (not shown). The sidechain nitrogens of Arg333 and Arg344 touch each other (3.0 Å). These characteristics are confirmed in 6nef. The presence of these cations deep within OmcS is plausible, since proteins of this size have, on average, several buried charges. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried. Burying charge seems to be an important factor in how evolution regulates protein stability. The buried contact between two usually-cationic sidechains of Arg333 and Arg344 is also plausible because, when buried, the positive charge of the guanidinium group can be greatly diminished due to dehydration and nearby positive charges. Although hydrated guanidinium retains more than half of its charge when the pH is below ~12 (its intrinsic pKa), dehydration due to burial decreases the pKa. Furthermore, the samples for cryo-electron microscopy were prepared at pH 10.5 (despite the pH being incorrectly stated as 7.0 in REMARK 245 of the PDB file). Other Findings & Conclusions References for the assertions below are cited in the journal publication. Seamless micrometer-long polymerization of hundreds of cytochromes is without precedent, to the knowledge of the authors. The filaments whose structure was determined here were obtained from electrode-grown cells. However, fumarate-grown cells produced filaments with similar sinusoidal morphology. The purified OmcS filaments have morphology and power spectra similar to cell-attached filaments previously thought to be type IV pili. Direct current electrical conductivity of individual wild type ~4 nm OmcS filaments was confirmed, and was comparable to previously reported filament conductivity values. Cells with the omcS gene deleted (ΔomcS) produced thinner (~1.7 nm) filaments that were smooth (not sinusoidal) and had electrical conductivity >100-fold lower than the OmcS filaments. ΔomcS cells can produce electrically conductive biofilms, but that conductivity might well depend on filaments of OmcZ, whose expression is known to increase in ΔomcS cells. Previous studies showed that PilA is required for export of OmcS. However, PilA was not found in the structure of the OmcS nanowires studied here. Thus, PilA appears to be required for production of OmcS nanowires, but not to be a structural component of those nanowires.

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See Also

• 3ucp: A list of all interactive 3D complements for publications from the Malvankar group.