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The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity. Human proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce viral infectivity. Here, the authors show that SERINC3 has architecture resembling non-ATP dependent lipid transporters and induces loss of membrane asymmetry correlated with changes in envelope conformation and loss of infectivity. [ABSTRACT FROM AUTHOR]

Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance. Developments in cryo-EM sample preparation and data collection are pivotal for structure determination. Fromm et al. present a 1.55 Å structure of the translating bacterial ribosome that provides new insights on its function and may allow for more precise structure-based drug design. [ABSTRACT FROM AUTHOR]

B1 cell-derived natural antibodies are non-specific polyreactive antibodies and can activate the complement pathway leading to lysis of enveloped virus particles before activation of the adaptive immune response. We investigated the relationship between natural antibody levels and treatment outcomes of 126 treatment-naïve chronic hepatitis B (CHB) patients, who underwent entecavir (ETV) treatment. Serum IgG1-3 and complement C3 levels were significantly higher in HBeAg-positive patients. In pre-treatment, IgG1 (odd ratios [OR] 2.3, p < 0.0001), IgG2 (OR 9.8, p < 0.0001), IgG3 (OR 7.4, p < 0.0001), and C3 (OR 7.2, p < 0.0001) were associated with HBeAg-positive patients. At baseline, IgG2 (OR 10.2, p = 0.025), IgG4, (OR 3.4, p = 0.026), and complement C1q (OR 5.0, p = 0.0068) were associated with seroconverters. Post-treatment levels of IgG1-4 and C3/C1q were also associated with HBeAg-positive patients and seroconverters. High levels of IgG2-4 and C1q were observed in seroconverters but not in virological responders. Thus, high pretreatment and post-treatment levels of natural antibody IgG1-4, complement C3, and/or C1q were significantly associated with HBeAg-positivity and HBeAg seroconverters in CHB patients with ETV treatment. These results suggest that the presence of preexisting host immunity against chronic hepatitis B is closely related to outcome of ETV treatment. [ABSTRACT FROM AUTHOR]

We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins. Single particle cryo-electron microscopy of membrane proteins is limited by their small size and difficulty to orient. Here the authors generate recombinant antibodies against the 12 kDa fusion partner BRIL domain from apocytochrome b562 to use them as plug and play fiducial marks for structure determination of BRIL fused membrane proteins. [ABSTRACT FROM AUTHOR]

Commonly, hepatitis E virus (HEV) sequences are genotyped phylogenetically using subgenomic sequences. This paper examines this practice with sequences from members of the species Orthohepevirus A. As the length of sequences becomes progressively shorter, the number of identical sequences in an alignment tends to increase; however, these sequences retain their genotypic identity down to 100 nucleotides in length. The best substitution models tend to become less parameterized, bootstrap support decreases, and trees created from short subgenomic fragments are less likely to be isomorphic with trees from longer subgenomic fragments or complete genome sequences. However, it is still possible to correctly genotype sequences using fragments as small as 200 nucleotides. While it is possible to correctly genotype sequences with short subgenomic sequences, the estimates of evolutionary relationships between genotypes degrade to such an extent that sequences below 1600 nucleotides long cannot be used reliably to study these relationships, and comparisons of trees from different subgenomic regions with little or no sequence overlap can be problematic. Subtyping may be done, but it requires a careful examination of the region to be used to ensure that it correctly resolves the subtypes. [ABSTRACT FROM AUTHOR]

A normally endemic form of viral hepatitis is the cause of major epidemic outbreaks in developing countries. This disease has a global distribution and has been referred to as water-borne, epidemic or enterically transmitted non-A, non-B hepatitis (ET-NANBH). Although the fecal-oral route of transmission predominates, person-toperson routes of exposure were also suggested in some epidemiologic studies. The disease has been documented as having an extremely high mortality in pregnant women (~20%). Sporadic cases of ET-NANBH, as well as imported travel exposures, have been reported in developed countries. Molecular cloning was hampered by the lack of a tissue culture system for virus propagation, however, an available animal model and a newly developed non-specific amplification procedure were used to clone and identify an exogenous cDNA (ET1.1) from a Burma-isolate infected animal. Molecular clones were also identified by immunoscreening of a cDNA library made from a fecal specimen collected from a Mexican outbreak of ET-NANBH. The isolation and sequencing of a set of overlapping cDNA clones had led to the recognition that this form of hepatitis is caused by a virus unlike any of the other viral hepatitis agents. The molecular characterization of HEV will lead to important pathobiologic insights and hasten the development of potentially useful diagnostic and therapeutic products for ET-NANBH. [ABSTRACT FROM AUTHOR]

Hepatitis is transmitted by a number of infectious agents. The epidemiological characterization of waterborne or enterically transmitted non-A, non-B hepatitis (ET-NANBH) is unique when compared with other known hepatitides. We have reported on the molecular cloning of a cDNA clone derived from the etiologic agent associated with ET-NANBH, the hepatitis E virus (HEV). The complete sequence of these first molecular clones, isolated from an HEV-infected human after passage in Macaca fascicularis (cynomolgus macaques), illustrates a distant relationship to other known positive-strand RNA viruses of plants and animals. The translated major open reading frame (ORF-1) from these clones indicates that this portion of the genome encodes a polyprotein with consensus sequences found in RNA-dependent RNA polymerase and ATP/GTP binding domains. The latter activity has been associated with putative helicases of positive-strand RNA viruses. These viral-encoded enzymatic activities identify this region and ORF-1 as containing at least two different nonstructural genes involved in HEV replication. Molecular clones obtained from two other geographically distinct HEV isolates demonstrated sequence heterogeneity in this nonstructural gene region. Further study will be required to elucidate the pathogenic significance (if any) of this observed divergence in the nonstructural region. [ABSTRACT FROM AUTHOR]