Henning Arlt, Xuewu Sui, Brayden Folger, Carson Adams, Xiao Chen, Roman Remme, Fred A. Hamprecht, Frank DiMaio, Maofu Liao, Joel M. Goodman, Robert V. Farese, and Tobias C. Walther. 2/24/2022. “Seipin forms a flexible cage at lipid droplet formation sites.” Nature Structural & Molecular Biology.Abstract
Lipid droplets (LDs) form in the endoplasmic reticulum by phase separation of neutral lipids. This process is facilitated by the seipin protein complex, which consists of a ring of seipin monomers, with a yet unclear function. Here, we report a structure of S. cerevisiae seipin based on cryogenic-electron microscopy and structural modeling data. Seipin forms a decameric, cage-like structure with the lumenal domains forming a stable ring at the cage floor and transmembrane segments forming the cage sides and top. The transmembrane segments interact with adjacent monomers in two distinct, alternating conformations. These conformations result from changes in switch regions, located between the lumenal domains and the transmembrane segments, that are required for seipin function. Our data indicate a model for LD formation in which a closed seipin cage enables triacylglycerol phase separation and subsequently switches to an open conformation to allow LD growth and budding.
Alex G. Johnson, Tanita Wein, Megan L. Mayer, Brianna Duncan-Lowey, Erez Yirmiya, Yaara Oppenheimer-Shaanan, Gil Amitai, Rotem Sorek, and Philip J. Kranzusch. 1/13/2022. “Bacterial gasdermins reveal an ancient mechanism of cell death.” Science, 375, 6577, Pp. 221-225. Publisher's VersionAbstract
Gasdermins are cell death proteins in mammals that form membrane pores in response to pathogen infection. Johnson et al. report that diverse bacteria encode structural and functional homologs of mammalian gasdermins. Like their mammalian counterparts, bacterial gasdermins are activated by caspase-like proteases, oligomerize into large membrane pores, and defend against pathogen—in this case, bacteriophage—infection. Proteolytic activation occurs through the release of a short inhibitory peptide, and many bacterial gasdermins are lipidated to facilitate membrane pore formation. Pyroptotic cell death, a central component of mammalian innate immunity, thus has a shared origin with an ancient antibacteriophage defense system. —SMH Bacteria encode gasdermins that are activated by dedicated proteases, defend from phage, and induce cell death. Gasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. We discovered gasdermin homologs encoded in bacteria that defended against phages and executed cell death. Structures of bacterial gasdermins revealed a conserved pore-forming domain that was stabilized in the inactive state with a buried lipid modification. Bacterial gasdermins were activated by dedicated caspase-like proteases that catalyzed site-specific cleavage and the removal of an inhibitory C-terminal peptide. Release of autoinhibition induced the assembly of large and heterogeneous pores that disrupted membrane integrity. Thus, pyroptosis is an ancient form of regulated cell death shared between bacteria and animals.
Alexander F. A. Keszei, Matthew C. J. Yip, Ta-Chien Hsieh, and Sichen Shao. 12/9/2021. “Structural insights into metazoan pretargeting GET complexes.” Nature Structural & Molecular Biology, 28, 12, Pp. 1029-1037. Publisher's VersionAbstract
Close coordination between chaperones is essential for protein biosynthesis, including the delivery of tail-anchored (TA) proteins containing a single C-terminal transmembrane domain to the endoplasmic reticulum (ER) by the conserved GET pathway. For successful targeting, nascent TA proteins must be promptly chaperoned and loaded onto the cytosolic ATPase Get3 through a transfer reaction involving the chaperone SGTA and bridging factors Get4, Ubl4a and Bag6. Here, we report cryo-electron microscopy structures of metazoan pretargeting GET complexes at 3.3–3.6þinspace}\AA. The structures reveal that Get3 helixþinspace}8 and the Get4 Cþinspace}terminus form a composite lid over the Get3 substrate-binding chamber that is opened by SGTA. Another interaction with Get4 prevents formation of Get3 helixþinspace}4, which links the substrate chamber and ATPase domain. Both interactions facilitate TA protein transfer from SGTA to Get3. Our findings show how the pretargeting complex primes Get3 for coordinated client loading and ER targeting.
Liudmila Andreeva, Liron David, Shaun Rawson, Chen Shen, Teerithveen Pasricha, Pablo Pelegrin, and Hao Wu. 12/3/2021. “NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation.” Cell. Publisher's Version
Katherine G. Nabel, Sarah A. Clark, Sundaresh Shankar, Junhua Pan, Lars E. Clark, Pan Yang, Adrian Coscia, Lindsay G. A. McKay, Haley H. Varnum, Vesna Brusic, Nicole V. Tolan, Guohai Zhou, Michaël Desjardins, Sarah E. Turbett, Sanjat Kanjilal, Amy C. Sherman, Anand Dighe, Regina C. LaRocque, Edward T. Ryan, Casey Tylek, Joel F. Cohen-Solal, Anhdao T. Darcy, Davide Tavella, Anca Clabbers, Yao Fan, Anthony Griffiths, Ivan R. Correia, Jane Seagal, Lindsey R. Baden, Richelle C. Charles, and Jonathan Abraham. 12/2/2021. “Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.” Science, Pp. eabl6251.Abstract
Many studies have examined the impact of SARS-CoV-2 variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
Haixia Zhou, Manal S Zaher, Johannes C Walter, and Alan Brown. 12/1/2021. “Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates.” Nucleic Acids Research. Publisher's VersionAbstract
When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then disassembled by the p97 ATPase, leading to replication termination. To avoid premature replisome disassembly, CRL2Lrr1 is only recruited to CMGs after they converge, but the underlying mechanism is unclear. Here, we use cryogenic electron microscopy to determine structures of recombinant Xenopus laevis CRL2Lrr1 with and without neddylation. The structures reveal that CRL2Lrr1 adopts an unusually open architecture, in which the putative substrate-recognition subunit, Lrr1, is located far from the catalytic module that catalyzes ubiquitin transfer. We further demonstrate that a predicted, flexible pleckstrin homology domain at the N-terminus of Lrr1 is essential to target CRL2Lrr1 to terminated CMGs. We propose a hypothetical model that explains how CRL2Lrr1’s catalytic module is positioned next to the ubiquitylation site on Mcm7, and why CRL2Lrr1 binds CMG only after replisomes converge.
Miao Gui, Hannah Farley, Priyanka Anujan, Jacob R. Anderson, Dale W. Maxwell, Jonathan B. Whitchurch, J. Josephine Botsch, Tao Qiu, Shimi Meleppattu, Sandeep K. Singh, Qi Zhang, James Thompson, Jane S. Lucas, Colin D. Bingle, Dominic P. Norris, Sudipto Roy, and Alan Brown. 10/28/2021. “De novo identification of mammalian ciliary motility proteins using cryo-EM.” Cell. Publisher's Version
Jun Zhang, Tianshu Xiao, Yongfei Cai, Christy L. Lavine, Hanqin Peng, Haisun Zhu, Krishna Anand, Pei Tong, Avneesh Gautam, Megan L. Mayer, Richard M. Walsh Jr., Sophia Rits-Volloch, Duane R. Wesemann, Wei Yang, Michael S. Seaman, Jianming Lu, and Bing Chen. 10/26/2021. “Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.” Science, Pp. eabl9463.Abstract
The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report the structure, function, and antigenicity of its full-length spike (S) trimer and those of the Gamma and Kappa variants and compare their characteristics with the G614, Alpha, and Beta variants. Delta S can fuse membranes more efficiently at low levels of cellular receptor ACE2, and its pseudotyped viruses infect target cells substantially faster than the other five variants, possibly accounting for its heightened transmissibility. Each variant shows different rearrangement of the antigenic surface of the N-terminal domain of the S protein, but only causes local changes in the receptor-binding domain (RBD), making the RBD a better target for therapeutic antibodies.
Yuri Iozzo (Egor Svidritskiy), Yu Qiu, Albert Xu, Anna Park, Maria Wendt, and Yanfeng Zhou. 10/4/2021. “Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering.” Antibody Therapeutics, 4, 4, Pp. 242-251. Publisher's VersionAbstract
Developing a biologic medicine requires successful decision making at early stages. Knowing structural information for discovery candidates greatly increases the probability of success.We have evaluated and integrated various structural biology and computation tools and established a cost-effective platform that allows us to obtain fast and accurate structural information for nearly all our biologics projects.We report four case studies selected from 38 projects and share how we integrate cryo-EM structure determination, computational modeling, and molecular dynamics simulation. With proper decision making and strategic planning, the platform allows to obtain results within days to weeks, including sub-100 kDa complexes.Our utilization of this differential approach and multiple software packages allows to manage priorities and resources to achieve goals efficiently. We demonstrate how to overcome particle orientation bias by altering complex composition. In several of our examples, we use glycan density and protein information to facilitate interpretation of low-resolution 3D maps.
François A. Thélot, Wenyi Zhang, KangKang Song, Chen Xu, Jing Huang, and Maofu Liao. 9/23/2021. “Distinct allosteric mechanisms of first-generation MsbA inhibitors.” Science.Abstract
ATP-binding cassette (ABC) transporters couple ATP hydrolysis to substrate transport across biological membranes. Although many are promising drug targets, their mechanisms of modulation by small molecule inhibitors remain largely unknown. Intriguingly, two first-generation inhibitors of the MsbA transporter, TBT1 and G247, induce opposite effects on ATP hydrolysis. Using single-particle cryo-electron microscopy and functional assays, we show that TBT1 and G247 bind adjacent yet separate pockets in the MsbA transmembrane domains. Two TBT1 molecules asymmetrically occupy the substrate binding site, leading to a collapsed inward-facing conformation with decreased distance between the nucleotide-binding domains (NBDs). In contrast, two G247 molecules symmetrically increases NBD distance in a wide inward-open state of MsbA. The divergent mechanisms of action of these MsbA inhibitors provide important insights into ABC transporter pharmacology.
Moritz Hunkeler, Cyrus Y. Jin, Michelle W. Ma, Julie K. Monda, Daan Overwijn, Eric J. Bennett, and Eric S. Fischer. 7/26/2021. “Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition.” Molecular Cell. Publisher's Version
Pei Tong, Avneesh Gautam, Ian W. Windsor, Meghan Travers, Yuezhou Chen, Nicholas Garcia, Noah B. Whiteman, Lindsay G. A. McKay, Nadia Storm, Lauren E. Malsick, Anna N. Honko, Felipe J.N. Lelis, Shaghayegh Habibi, Simon Jenni, Yongfei Cai, Linda J. Rennick, W. Paul Duprex, Kevin R. McCarthy, Christy L. Lavine, Teng Zuo, Junrui Lin, Adam Zuiani, Jared Feldman, Elizabeth A. MacDonald, Blake M. Hauser, Anthony Griffths, Michael S. Seaman, Aaron G. Schmidt, Bing Chen, Donna Neuberg, Goran Bajic, Stephen C. Harrison, and Duane R. Wesemann. 7/22/2021. “Memory B Cell Repertoire for Recognition of Evolving SARS-CoV-2 Spike.” Cell. Publisher's Version
Yongfei Cai, Jun Zhang, Tianshu Xiao, Christy L. Lavine, Shaun Rawson, Hanqin Peng, Haisun Zhu, Krishna Anand, Pei Tong, Avneesh Gautam, Shen Lu, Sarah M. Sterling, Richard M. Walsh, Sophia Rits-Volloch, Jianming Lu, Duane R. Wesemann, Wei Yang, Michael S. Seaman, and Bing Chen. 6/24/2021. “Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants.” Science. Publisher's VersionAbstract
Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains in the COVID-19 pandemic. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Amino acid substitutions in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement may account for the increased transmissibility. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, making it resistant to some potent neutralizing antibodies. These findings provide structural details on how SARS-CoV-2 has evolved to enhance viral fitness and immune evasion.
Yun Quan, Stephen M. Hinshaw, Pang-Che Wang, Stephen C. Harrison, and Huilin Zhou. 6/3/2021. “Ctf3/CENP-I provides a docking site for the desumoylase Ulp2 at the kinetochore.” Journal of Cell Biology, 220, 8. Publisher's VersionAbstract
The step-by-step process of chromosome segregation defines the stages of the cell cycle. In eukaryotes, signals controlling these steps converge upon the kinetochore, a multiprotein assembly that connects spindle microtubules to chromosomal centromeres. Kinetochores control and adapt to major chromosomal transactions, including replication of centromeric DNA, biorientation of sister centromeres on the metaphase spindle, and transit of sister chromatids into daughter cells during anaphase. Although the mechanisms that ensure tight microtubule coupling at anaphase are at least partly understood, kinetochore adaptations that support other cell cycle transitions are not. We report here a mechanism that enables regulated control of kinetochore sumoylation. A conserved surface of the Ctf3/CENP-I kinetochore protein provides a binding site for Ulp2, the nuclear enzyme that removes SUMO chains from modified substrates. Ctf3 mutations that disable Ulp2 recruitment cause elevated inner kinetochore sumoylation and defective chromosome segregation. The location of the site within the assembled kinetochore suggests coordination between sumoylation and other cell cycle–regulated processes.
Humayun Sharif, L. Robert Hollingsworth, Andrew R. Griswold, Jeffrey C. Hsiao, Qinghui Wang, Daniel A. Bachovchin, and Hao Wu. 5/20/2021. “Dipeptidyl peptidase 9 sets a threshold for CARD8 inflammasome formation by sequestering its active C-terminal fragment.” Immunity. Publisher's VersionAbstract
Summary CARD8 detects intracellular danger signals and forms a caspase-1 activating inflammasome. Like the related inflammasome sensor NLRP1, CARD8 autoprocesses into noncovalently associated N-terminal (NT) and C-terminal (CT) fragments and binds the cellular dipeptidyl peptidases DPP8 and 9 (DPP8/9). Certain danger-associated signals, including the DPP8/9 inhibitor Val-boroPro (VbP) and HIV protease, induce proteasome-mediated NT degradation and thereby liberate the inflammasome-forming CT. Here, we report cryoelectron microscopy (cryo-EM) structures of CARD8 bound to DPP9, revealing a repressive ternary complex consisting of DPP9, full-length CARD8, and CARD8-CT. Unlike NLRP1-CT, CARD8-CT does not interact with the DPP8/9 active site and is not directly displaced by VbP. However, larger DPP8/9 active-site probes can directly weaken this complex in vitro, and VbP itself nevertheless appears to disrupt this complex, perhaps indirectly, in cells. Thus, DPP8/9 inhibitors can activate the CARD8 inflammasome by promoting CARD8 NT degradation and by weakening ternary complex stability.
Shiyu Xia, Zhibin Zhang, Venkat Giri Magupalli, Juan Lorenzo Pablo, Ying Dong, Setu M. Vora, Longfei Wang, Tian-Min Fu, Matthew P. Jacobson, Anna Greka, Judy Lieberman, Jianbin Ruan, and Hao Wu. 4/21/2021. “Gasdermin D pore structure reveals preferential release of mature interleukin-1.” Nature. Publisher's VersionAbstract
As organelles of the innate immune system, inflammasomes activate caspase-1 and other inflammatory caspases that cleave gasdermin D (GSDMD). Caspase-1 also cleaves inactive precursors of the interleukin (IL)-1 family to generate mature cytokines such as IL-1$\beta$ and IL-18. Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis1–9. Here we report cryo-electron microscopy structures of the pore and the prepore of GSDMD. These structures reveal the different conformations of the two states, as well as extensive membrane-binding elements including a hydrophobic anchor and three positively charged patches. The GSDMD pore conduit is predominantly negatively charged. By contrast, IL-1 precursors have an acidic domain that is proteolytically removed by caspase-110. When permeabilized by GSDMD pores, unlysed liposomes release positively charged and neutral cargoes faster than negatively charged cargoes of similar sizes, and the pores favour the passage of IL-1$\beta$ and IL-18 over that of their precursors. Consistent with these findings, living–-but not pyroptotic–-macrophages preferentially release mature IL-1$\beta$ upon perforation by GSDMD. Mutation of the acidic residues of GSDMD compromises this preference, hindering intracellular retention of the precursor and secretion of the mature cytokine. The GSDMD pore therefore mediates IL-1 release by electrostatic filtering, which suggests the importance of charge in addition to size in the transport of cargoes across this large channel.
Helena M. Schnell, Richard M. Walsh, Shaun Rawson, Mandeep Kaur, Meera K. Bhanu, Geng Tian, Miguel A. Prado, Angel Guerra-Moreno, Joao A. Paulo, Steven P. Gygi, Jeroen Roelofs, Daniel Finley, and John Hanna. 4/12/2021. “Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis.” Nature Structural & Molecular Biology. Publisher's VersionAbstract
The proteasome mediates most selective protein degradation. Proteolysis occurs within the 20S core particle (CP), a barrel-shaped chamber with an $\alpha$7$\beta$7$\beta$7$\alpha$7 configuration. CP biogenesis proceeds through an ordered multistep pathway requiring five chaperones, Pba1–4 and Ump1. Using Saccharomyces cerevisiae, we report high-resolution structures of CP assembly intermediates by cryogenic-electron microscopy. The first structure corresponds to the 13S particle, which consists of a complete $\alpha$-ring, partial $\beta$-ring ($\beta$2–4), Ump1 and Pba1/2. The second structure contains two additional subunits ($\beta$5–6) and represents a later pre-15S intermediate. These structures reveal the architecture and positions of Ump1 and $\beta$2/$\beta$5 propeptides, with important implications for their functions. Unexpectedly, Pba1's N terminus extends through an open CP pore, accessing the CP interior to contact Ump1 and the $\beta$5 propeptide. These results reveal how the coordinated activity of Ump1, Pba1 and the active site propeptides orchestrate key aspects of CP assembly.
L. Robert Hollingsworth, Humayun Sharif, Andrew R. Griswold, Pietro Fontana, Julian Mintseris, Kevin B. Dagbay, Joao A. Paulo, Steven P. Gygi, Daniel A. Bachovchin, and Hao Wu. 3/18/2021. “DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation.” Nature. Publisher's VersionAbstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 1 (NLRP1) is an inflammasome sensor that mediates the activation of caspase-1 to induce cytokine maturation and pyroptosis1–4. Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin4–6. NLRP1 contains a function-to-find domain that auto-proteolyses into noncovalently associated subdomains7–9, and proteasomal degradation of the repressive N-terminal fragment of NLRP1 releases its inflammatory C-terminal fragment (NLRP1 CT)10,11. Cytosolic dipeptidyl peptidases 8 and 9 (hereafter, DPP8/DPP9) both interact with NLRP1, and small-molecule inhibitors of DPP8/DPP9 activate NLRP1 by mechanisms that are currently unclear10,12–14. Here we report cryo-electron microscopy structures of the human NLRP1–DPP9 complex alone and with Val-boroPro (VbP), an inhibitor of DPP8/DPP9. The structures reveal a ternary complex that comprises DPP9, full-length NLRP1 and the NLRPT CT. The binding of the NLRP1 CT to DPP9 requires full-length NLRP1, which suggests that NLRP1 activation is regulated by the ratio of NLRP1 CT to full-length NLRP1. Activation of the inflammasome by ectopic expression of the NLRP1 CT is consistently rescued by co-expression of autoproteolysis-deficient full-length NLRP1. The N terminus of the NLRP1 CT inserts into the DPP9 active site, and VbP disrupts this interaction. Thus, VbP weakens the NLRP1–DPP9 interaction and accelerates degradation of the N-terminal fragment10 to induce inflammasome activation. Overall, these data demonstrate that DPP9 quenches low levels of NLRP1 CT and thus serves as a checkpoint for activation of the NLRP1 inflammasome.
Jun Zhang, Yongfei Cai, Tianshu Xiao, Jianming Lu, Hanqin Peng, Sarah M. Sterling, Richard M. Walsh, Sophia Rits-Volloch, Haisun Zhu, Alec N. Woosley, Wei Yang, Piotr Sliz, and Bing Chen. 3/16/2021. “Structural impact on SARS-CoV-2 spike protein by D614G substitution.” Science. Publisher's VersionAbstract
Substitution for aspartic acid by glycine at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. We report here cryo-EM structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations differing primarily by the position of one receptor-binding domain. A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer, effectively increasing the number of functional spikes and enhancing infectivity, and to modulate structural rearrangements for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.
Meng Zhang, Miao Gui, Zi-Fu Wang, Christoph Gorgulla, James J. Yu, Hao Wu, Zhen-yu J. Sun, Christoph Klenk, Lisa Merklinger, Lena Morstein, Franz Hagn, Andreas Plückthun, Alan Brown, Mahmoud L. Nasr, and Gerhard Wagner. 2/25/2021. “Cryo-EM structure of an activated GPCR–G protein complex in lipid nanodiscs.” Nature Structural & Molecular Biology, 28, 3, Pp. 258-267. Publisher's VersionAbstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals. Although several structures have been solved for GPCR–G protein complexes, few are in a lipid membrane environment. Here, we report cryo-EM structures of complexes of neurotensin, neurotensin receptor 1 and G$\alpha$i1$\beta$1$\gamma$1 in two conformational states, resolved to resolutions of 4.1 and 4.2þinspace}\AA. The structures, determined in a lipid bilayer without any stabilizing antibodies or nanobodies, reveal an extended network of protein–protein interactions at the GPCR–G protein interface as compared to structures obtained in detergent micelles. The findings show that the lipid membrane modulates the structure and dynamics of complex formation and provide a molecular explanation for the stronger interaction between GPCRs and G proteins in lipid bilayers. We propose an allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling.