G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G proteinindependent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms § Correspondence to H. Eric Xu: Eric.Xu@vai.org. * These authors contributed equally.Contributions: Y.K. initiated the project, developed the expression and purification methods for rhodopsin-arrestin complex, and bulk-purified expression constructs and proteins used in LCP crystallization for the SFX method; X.E.Z. collected the synchrotron data, helped with the SFX data collection, processed the data, and solved the structures; X.G. expressed and purified rhodopsinarrestin complexes, characterized their binding and thermal stability, discovered the initial crystallization conditions with 9.7 MAG, prepared most crystals for synchrotron data collection, prepared all crystals for the final data collection by SFX, helped with SFX data collection, and established the initial cross-linking method for the rhodopsin-arrestin complex; Y.H. designed and performed Tango assays and disulfide bond cross-linking experiments; C.Z. developed the mammalian expression methods; P.W.dW helped with XFEL data processing and performed computational experiments; J.K., M.H.E.T., K. M. S-P., K. P., J. M., Y.J., X.Y.Z., and Q.C. performed cell culture, mutagenesis, protein purification, rhodopsin-arrestin binding experiments; W.L. and A.I. grew crystals and collected synchrotron data at APS and SFX data at LCLS, G.W.H. and Q.X. determined and validated the structure. Z.Z. and V.K. constructed the full model, the phosphorylated rhodopsin-arrestin model, and help writing the paper; D.W., S.L., D.J., C.K., Sh.B., and N.A. Z. helped with XFEL data collection and initial data analysis; S.B., M.M., and G.J.W. set up the XFEL experiment, performed the data collection, and commented on the paper. A.B., T.W., C.G., O.Y., and H.C. helped with XFEL data collection and data analysis, processed the data and helped with structure validation. G.M. W., B.P., and P.G. performed HDX experiments and helped with manuscript writing. J.L. helped initiate this collaborative project and with writing the paper. M.W. collected the 7.7 Å dataset at Swiss Light Source. A.M.,...

The pandemic of coronavirus disease 2019 (COVID-19) is changing the world like never before. This crisis is unlikely contained in the absence of effective therapeutics or vaccine. The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology, inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development. In this study, we sought to provide structural frameworks for PLpro inhibitor design. We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111S, which shares many structural features of SARS-CoV PLpro. This crystal form has unique packing, high solvent content and reasonable resolution 2.5 Å, hence provides a good possibility for fragment-based screening using crystallographic approach. We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture. We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARS-CoV-2 with the IC 50 of 2.2 ± 0.3 μmol/L. We then determined the structure of SARS-CoV-2 PLpro complexed by GRL0617 to 2.6 Å, showing the inhibitor accommodates the S3–S4 pockets of the substrate binding cleft. The binding of GRL0617 induces closure of the BL2 loop and narrows the substrate binding cleft, whereas the binding of a tetrapeptide substrate enlarges the cleft. Hence, our results suggest a mechanism of GRL0617 inhibition, that GRL0617 not only occupies the substrate pockets, but also seals the entrance to the substrate binding cleft hence prevents the binding of the LXGG motif of the substrate.

Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus (HCV) from two crystal forms have been determined. Similar to the three-dimensional structures of HCV polymerase genotype 1b and other known polymerases, the structures of the HCV polymerase genotype 2a in both crystal forms can be depicted in the classical right-hand arrangement with fingers, palm, and thumb domains. The main structural differences between the molecules in the two crystal forms lie at the interface of the fingers and thumb domains. The relative orientation of the thumb domain with respect to the fingers and palm domains and the ␤-flap region is altered. Structural analysis reveals that the NS5B polymerase in crystal form I adopts a "closed" conformation that is believed to be the active form, whereas NS5B in crystal form II adopts an "open" conformation and is thus in the inactive form. In addition, we have determined the structures of two NS5B polymerase/non-nucleoside inhibitor complexes. Both inhibitors bind at a common binding site, which is nearly 35 Å away from the polymerase active site and is located in the thumb domain. The binding pocket is predominantly hydrophobic in nature, and the enzyme inhibitor complexes are stabilized by hydrogen bonding and van der Waals interactions. Inhibitors can only be soaked in crystal form I and not in form II; examination of the enzyme-inhibitor complex reveals that the enzyme has undergone a dramatic conformational change from the form I (active) complex to the form II (inactive).

X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNAdependent RNA polymerase have been determined to 2.0 and 2.9 Å resolution. These noncompetitive inhibitors bind to the same site on the protein, ϳ35 Å from the active site. The common features of binding include a large hydrophobic region and two hydrogen bonds between both oxygen atoms of a carboxylate group on the inhibitor and two main chain amide nitrogen atoms of Ser 476 and Tyr 477 on NS5B. The inhibitor-binding site lies at the base of the thumb domain, near its interface with the C-terminal extension of NS5B. The location of this inhibitor-binding site suggests that the binding of these inhibitors interferes with a conformational change essential for the activity of the polymerase. Hepatitis C virus (HCV)1 infects about 3% of the world's human population. HCV infection can develop into chronic hepatitis, which, in some cases, causes cirrhosis of the liver, eventually leading to hepatocellular carcinoma (1). There is no vaccine against HCV currently, and no generally effective therapy for all genotypes of HCV is available. At the present time, the use of recombinant interferon ␣-2a, ␣-2b, "consensus" interferon, and pegylated interferon ␣-2b either in monotherapy or in combination with ribavirin is the only approved therapy available (2). However, limited efficacy and some adverse side effects are associated with these therapies (3). Therefore, the development of HCV-specific antiviral agents is needed urgently.Extensive studies have been done to understand the structures and functions of the individual components of the HCVencoded polyprotein (structural proteins C, E1, and E2 and nonstructural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B) (4 -6). Among them, NS2, NS3 protease and helicase, and NS5B RNA-dependent RNA polymerase are essential enzymes for the replication of HCV. The high resolution crystal structures of NS3 protease (7-9) and helicase domains (10, 11) and NS5B polymerase (12-14) have been determined by crystallographic methods in the past 5 years. These enzymes are potential targets for structure-based drug design. The inhibitors of NS3 protease and, in some cases, corresponding structures of NS3 protease/inhibitor complexes have been reported recently (15). In the case of HCV NS5B polymerase, both nucleoside and non-nucleoside inhibitors have been discovered in recent years (16). 3TC (2Ј-deoxy-3Ј-thiacytidine proprietary compound lamivudine) triphosphate has been reported to have a weak inhibitory effect with a 50% inhibitory concentration (IC 50 ) of 180 M (17), whereas numerous non-nucleoside compounds have been documented to possess relatively potent anti-NS5B activity. Examples include specific rhodanines and barbituric acid derivatives, many of which were found to exhibit anti-NS5B activity with IC 50 values below 1 M (18, 19). Classes of dihydroxypyrimidine carboxylic acids and diketoacid derivatives were claimed as well with IC 50 values within the submicromolar range for the latt...

Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.

Structure of EV71 2C unveils the structural basis of the functional mechanism of carboxyl terminus–mediated self-oligomerization.

Middle East respiratory syndrome coronavirus (MERS-CoV) remains a threat to public health worldwide; however, effective vaccine or drug against CoVs remains unavailable. CoV helicase is one of the three evolutionary most conserved proteins in nidoviruses, thus making it an important target for drug development. We report here the first structure of full-length coronavirus helicase, MERS-CoV nsp13. MERS-CoV helicase has multiple domains, including an N-terminal Cys/His rich domain (CH) with three zinc atoms, a beta-barrel domain and a C-terminal SF1 helicase core with two RecA-like subdomains. Our structural analyses show that while the domain organization of nsp13 is conserved throughout nidoviruses, the individual domains of nsp13 are closely related to the equivalent eukaryotic domains of Upf1 helicases. The most distinctive feature differentiating CoV helicases from eukaryotic Upf1 helicases is the interaction between CH domain and helicase core.

We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.