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The structural characterization of the NS3-like helicase of a segmented virus from the Flaviviridae is reported., Alongshan virus (ALSV) is an emerging human pathogen that was identified in China and rapidly spread to the European continent in 2019, raising concerns about public health. ALSV belongs to the distinct Jingmenvirus group within the Flaviviridae family with segmented RNA genomes. While segments 2 and 4 of the ALSV genome encode the VP1–VP3 proteins of unknown origin, segments 1 and 3 encode the NS2b–NS3 and NS5 proteins, which are related to Flavivirus nonstructural proteins, suggesting an evolutionary link between segmented and unsegmented viruses within the Flaviviridae family. Here, the enzymatic activity of the ALSV NS3-like helicase (NS3-Hel) was characterized and its crystal structure was determined to 2.9 Å resolution. ALSV NS3-Hel exhibits an ATPase activity that is comparable to those measured for Flavivirus NS3 helicases. The structure of ALSV NS3-Hel exhibits an overall fold similar to those of Flavivirus NS3 helicases. Despite the limited amino-acid sequence identity between ALSV NS3-Hel and Flavivirus NS3 helicases, structural features at the ATPase active site and the RNA-binding groove remain conserved in ALSV NS3-Hel. These findings provide a structural framework for drug design and suggest the possibility of developing a broad-spectrum antiviral drug against both Flavivirus and Jingmenvirus.

Advantages of using a wavelength of 2.7 Å over a wavelength of 1.9 Å for native single-wavelength anomalous dispersion phasing are presented, and potentials of using a wavelength of 3.3 Å are discussed., Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

Gram-negative bacteria utilize the type III secretion system (T3SS) to inject effector proteins into the host cell cytoplasm, where they subvert cellular functions and assist pathogen invasion. The conserved type III-associated ATPase is critical for the separation of chaperones from effector proteins, the unfolding of effector proteins and translocating them through the narrow channel of the secretion apparatus. However, how ATP hydrolysis is coupled to the mechanical work of the enzyme remains elusive. Herein, we present a complete description of nucleoside triphosphate binding by surface presentation antigens 47 (Spa47) from Shigella flexneri, based on crystal structures containing ATPγS, a catalytic magnesium ion and an ordered water molecule. Combining the crystal structures of Spa47-ATPγS and unliganded Spa47, we propose conformational changes in Spa47 associated with ATP binding, the binding of ATP induces a conformational change of a highly conserved luminal loop, facilitating ATP hydrolysis by the Spa47 ATPase. Additionally, we identified a specific hydrogen bond critical for ATP recognition and demonstrated that, while ATPγS is an ideal analog for probing ATP binding, AMPPNP is a poor ATP mimic. Our findings provide structural insight pertinent for inhibitor design.

The new mineral sharyginite, Ca3TiFe2O8 (P21ma, Z = 2, a = 5.423(2) &Aring, b = 11.150(8) &Aring, c = 5.528(2) &Aring, V = 334.3(3) &Aring, 3), a member of the anion deficient perovskite group, was discovered in metacarbonate xenoliths in alkali basalt from the Caspar quarry, Bellerberg volcano, Eifel, Germany. In the holotype specimen, sharyginite is widespread in the contact zone of xenolith with alkali basalt. Sharyginite is associated with fluorellestadite, cuspidine, brownmillerite, rondorfite, larnite and minerals of the chlormayenite-wadalite series. The mineral usually forms flat crystals up to 100 &micro, m in length, which are formed by pinacoids {100}, {010} and {001}. Crystals are flattened on (010). Sharyginite is dark brown, opaque with a brown streak and has a sub-metallic lustre. In reflected light, it is light grey and exhibits rare yellowish-brown internal reflections. The calculated density of sharyginite is 3.943 g&middot, cm-3. The empirical formula calculated on the basis of 8 O apfu is Ca3.00(Fe3+1.00Ti4+0.86Mn4+0.11Zr0.01Cr3+0.01Mg0.01)&Sigma, 2(Fe3+0.76Al0.20Si0.04)&Sigma, 1.00O8. The crystal structure of sharyginite, closely related to shulamitite Ca3TiFeAlO8 structure, consists of double layers of corner-sharing (Ti, Fe3+) O6 octahedra, which are separated by single layers of (Fe3+O4) tetrahedra. We suggest that sharyginite formed after perovskite at high-temperature conditions &gt, 1000&deg, C.

Ariegilatite, BaCa12(SiO4)4(PO4)2F2O (R 3 ¯ m, a = 7.1551(6) Å, c = 41.303(3) Å, V = 1831.2(3) Å3, Z = 3), is a new member of the nabimusaite group exhibiting a modular intercalated antiperovskite structure derived from hatrurite. It was found in a few outcrops of pyrometamorphic rocks of the Hatrurim Complex located in the territories of Israel, Palestine and Jordan. The holotype specimen is an altered spurrite marble from the Negev Desert near Arad city, Israel. Ariegilatite is associated with spurrite, calcite, brownmillerite, shulamitite, CO3-bearing fluorapatite, fluormayenite-fluorkyuygenite and a potentially new mineral, Ba2Ca18(SiO4)6(PO4)3(CO3)F3O. Ariegilatite is overgrown and partially replaced by stracherite, BaCa6(SiO4)2[(PO4)(CO3)]F. The mineral forms flat disc-shaped crystals up to 0.5 mm in size. It is colorless, transparent, with white steaks and vitreous luster. Optically, ariegilatite is uniaxial, negative: ω = 1.650(2), ε = 1.647(2) (λ = 589 nm). The mean composition of the holotype ariegilatite, (Ba0.98K0.01Na0.01)Σ1(Ca11.77Na0.08Fe2+0.06Mn2+0.05Mg0.04)Σ12(Si3.95Al0.03Ti0.02)Σ4(P1.70C0.16Si0.10S6+0.03V0.01)Σ2F2.04O0.96, is close to the end-member formula. The structure of ariegilatite is described as a stacking of the two modules {F2OCa12(SiO4)4}4+ and {Ba(PO4)2}4− along (001). Ariegilatite, as well as associated stracherite, are high-temperature alteration products of minerals of an early clinker-like association. These alterations took place under the influence of pyrometamorphism by-products, such as gases and fluids generated by closely-spaced combustion foci.

It is more than 80 years since Gratia first described ‘a remarkable antagonism between two strains ofEscherichia coli’. Shown subsequently to be due to the action of proteins (or peptides) produced by one bacterium to kill closely related species with which it might be cohabiting, such bacteriocins have since been shown to be commonplace in the internecine warfare between bacteria. Bacteriocins have been studied primarily from the twin perspectives of how they shape microbial communities and how they penetrate bacteria to kill them. Here, we review the modes of action of a family of bacteriocins that cleave nucleic acid substrates inE. coli, known collectively as nuclease colicins, and the specific immunity (inhibitor) proteins that colicin-producing organisms make in order to avoid committing suicide. In a process akin to targeting in mitochondria, nuclease colicins engage in a variety of cellular associations in order to translocate their cytotoxic domains through the cell envelope to the cytoplasm. As well as informing on the process itself, the study of nuclease colicin import has also illuminated functional aspects of the host proteins they parasitize. We also review recent studies where nuclease colicins and their immunity proteins have been used as model systems for addressing fundamental problems in protein folding and protein–protein interactions, areas of biophysics that are intimately linked to the role of colicins in bacterial competition and to the import process itself.

The structure of the cytosolic C-terminal domain of nonstructural protein 4 from feline coronavirus has been determined and analyzed., Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26–31 kb) encodes 15–16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication–transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain (∼100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8 Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P43. The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly α-helical content displaying a unique fold that could be engaged in protein–protein interactions.

Threading Through Protein antibiotics (bacteriocins) are frequently deployed by Gram-negative bacteria to combat competitors, a trait common in pathogens such as Escherichia coli, Yersinia pestis, Pseudomonas aeruginosa, Xanthomonas campestris , and Klebsiella pneumonia . As a result, bacteriocins are being developed as species-specific antibacterials. Bacteriocins must establish a translocon at the bacterial outer membrane in order to translocate into cells. Working in E. coli , Housden et al. (p. 1570 ) describe how the deoxyribonuclease, colicin E9, crosses the bacterial cell membrane by threading through a porin.

Staphylococcus aureus and Staphylococcus epidermidis form communities (called biofilms) on inserted medical devices, leading to infections that affect many millions of patients worldwide and cause substantial morbidity and mortality. As biofilms are resistant to antibiotics, device removal is often required to resolve the infection. Thus, there is a need for new therapeutic strategies and molecular data that might assist their development. Surface proteins S. aureus surface protein G (SasG) and accumulation-associated protein ( S. epidermidis ) promote biofilm formation through their “B” regions. B regions contain tandemly arrayed G5 domains interspersed with approximately 50 residue sequences (herein called E) and have been proposed to mediate intercellular accumulation through Zn 2+ -mediated homodimerization. Although E regions are predicted to be unstructured, SasG and accumulation-associated protein form extended fibrils on the bacterial surface. Here we report structures of E–G5 and G5–E–G5 from SasG and biophysical characteristics of single and multidomain fragments. E sequences fold cooperatively and form interlocking interfaces with G5 domains in a head-to-tail fashion, resulting in a contiguous, elongated, monomeric structure. E and G5 domains lack a compact hydrophobic core, and yet G5 domain and multidomain constructs have thermodynamic stabilities only slightly lower than globular proteins of similar size. Zn 2+ does not cause SasG domains to form dimers. The work reveals a paradigm for formation of fibrils on the 100-nm scale and suggests that biofilm accumulation occurs through a mechanism distinct from the “zinc zipper.” Finally, formation of two domains by each repeat (as in SasG) might reduce misfolding in proteins when the tandem arrangement of highly similar sequences is advantageous.