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N1 - Funding Information:Funding: This research was funded by grants from the National Institute of Neurological Disorders and Stroke (NINDS) and National Institute of Aging (NIA) of the National Institute of Health (NIH) under award numbers R01NS088645, RF1NS112719, R03AG064266, and R01NS094535, and the Houston Methodist Research Institute funds.Publisher Copyright: MDPI. All rights reserved.

In this article, we describe an example of molecular replacement in which we use atomic models to interpret electron-density maps determined using single-particle electron-microscopy data. The method of combining high-resolution structural information from crystallography with lower resolution structures obtained through electron microscopy is referred to as the hybrid method. We will briefly explain how the APC/C functions to regulate the cell cycle before describing our approach to determining a pseudo-atomic structure of the complex.

One striking feature of the APC/C is that only four proteins are involved in directly recognizing target proteins and in catalyzing the assembly of a polyubiquitin chain onto the substrate. All other subunits, which account for 80% of the mass of the APC/C, provide scaffolding functions to organize the catalytic and substrate-recognition subunits. Another feature of the APC/C is that many of the scaffolding proteins are structurally related. In human APC/C there are four TPR subunits that have very simple architectures based on multiple contiguous copies of a 34-amino-acid sequence motif called the tetratricopeptide (TPR) motif. The smaller TPR accessory subunits stabilize the larger TPR subunits and also mediate inter-TPR interactions. In isolation, these TPR accessory subunits are disordered and they only assume a defined conformation when associated with the TPR subunits.

Our research has been aimed at obtaining atomic structures of individual APC/C subunits and to define how these subunits are organized within the whole complex as a means to understand how the APC/C recognizes its substrates and catalyses the assembly of polyubiquitin chains. To apply the hybrid approach to generate pseudo-atomic structures of the APC/C we have determined atomic models of most of the large APC/C subunits through a combination of protein crystallography and homology modelling. We now have atomic models for most of the large APC/C subunits except for Apc4 and the N-terminus of Apc1. We also lack structural information on some of the smaller APC/C subunits (Table 1).

Conceived and designed the experiments: JZ LX PZ. Performed the experiments: HZ JZ HF RL JW. Analyzed the data: HZ JZ LX PZ. Contributed reagents/materials/analysis tools: JW. Wrote the paper: HZ JZ PZ. Supervised the project: LX PZ.

Hemocyanins (Hcs) of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs). In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8  cryo-electron microscopy (cryo-EM) structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV) infected abalone (Halitotis diversicolor), and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1). Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs) present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens.

Hcs from different organisms display diversified structures. In arthropods, for instance, Hcs exist as hexamers as well as multihexamers, whereas in molluscan, Hcs were shown to display deca-, dideca-, as well as tridecameric forms [1], [2], [5]. As the oxygen carrier and transporter in Halitotis diversicolor, each functional unit (FU) of H. diversicolor Hemocyanin contains an oxygen-binding center, which contains two copper ions directly ligated to the side chains of three conserved histidines surrounding the copper ions [6], [7]. Upon contact with oxygen, the Cu ion pair in each FU binds to one peroxide ion, turning the Cu(I)-Cu(I) deoxygenated state into an oxidated Cu(II)-Cu(II) state [8], [9], after which the colorless Hc turns blue.

Although the structure of native form molluscan Hc had been reported [2], [23], the structure basis how molluscan Hc switches its role from mainly acting as an oxygen carrier to becoming a PO remains poorly understood. In this study, we found that isomeric Hcs from abalone infected with abalone shriveling syndrome-associated virus (AbSV) [24] exhibit strong PO activity in the absence of in vitro allosteric effectors. The architecture of isomeric form of Hc from AbSV infected abalone turns into a more relaxed state compared with native form of Hc. Our results suggest that the decrease in the interactions between FUs in isomeric Hc contributes to the activation of PO activity of HC. As a result, the Hc switches its role from being mainly an oxygen carrier to functioning in its capacity as an active PO, required for the proper initiation of a mollusk innate immune response. e24fc04721

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