Xuewu Sui, Kun Wang, Nina L. Gluchowski, Shane D. Elliott, Maofu Liao, Tobias C. Walther, and Robert V. Farese. 5/13/2020. “Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme.” Nature. Publisher's VersionAbstract
Triacylglycerols store metabolic energy in organisms and have industrial uses as foods and fuels. Excessive accumulation of triacylglycerols in humans causes obesity and is associated with metabolic diseases1. Triacylglycerol synthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes2–4, the structures and catalytic mechanisms of which remain unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at approximately 3.0 \AA resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at approximately 3.2 \AA shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction centre is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density–-possibly representing an acyl-acceptor molecule–-is located within the reaction centre, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, provide the basis for a model of the catalysis of triacylglycerol synthesis by DGAT.
Benjamin J Orlando and Maofu Liao. 2020. “ABCG2 transports anticancer drugs via a closed-to-open switch.” Nat Commun, 11, 1, Pp. 2264.Abstract
ABCG2 is an ABC transporter that extrudes a variety of compounds from cells, and presents an obstacle in treating chemotherapy-resistant cancers. Despite recent structural insights, no anticancer drug bound to ABCG2 has been resolved, and the mechanisms of multidrug transport remain obscure. Such a gap of knowledge limits the development of novel compounds that block or evade this critical molecular pump. Here we present single-particle cryo-EM studies of ABCG2 in the apo state, and bound to the three structurally distinct chemotherapeutics. Without the binding of conformation-selective antibody fragments or inhibitors, the resting ABCG2 adopts a closed conformation. Our cryo-EM, biochemical, and functional analyses reveal the binding mode of three chemotherapeutic compounds, demonstrate how these molecules open the closed conformation of the transporter, and establish that imatinib is particularly effective in stabilizing the inward facing conformation of ABCG2. Together these studies reveal the previously unrecognized conformational cycle of ABCG2.
Xudong Wu, Marc Siggel, Sergey Ovchinnikov, Wei Mi, Vladimir Svetlov, Evgeny Nudler, Maofu Liao, Gerhard Hummer, and Tom A. Rapoport. 2020. “Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.” Science, 368, 6489. Publisher's VersionAbstract
Misfolded endoplasmic reticulum (ER) proteins are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome in a process known as ER-associated protein degradation (ERAD). ERAD of misfolded luminal ER proteins (ERAD-L) is mediated by the Hrd1 complex, composed of the ubiquitin ligase Hrd1 and four additional proteins (Hrd3, Der1, Usa1, and Yos9). Wu et al. report a cryo–electron microscopy structure of the active Hrd1 complex from yeast and, based on this structure, developed a model for how substrates are recognized and retrotranslocated. They propose that Hrd3 and Yos9 jointly create a luminal binding site for misfolded glycoproteins. Hrd1 and Der1 form “half-channels” juxtaposed in a thinned section of the ER membrane, which allows a polypeptide loop of an ERAD-L substrate to move through it.Science, this issue p. eaaz2449INTRODUCTIONProtein homeostasis in the endoplasmic reticulum (ER) is maintained by a quality control system. When a newly synthesized ER protein misfolds, it is ultimately retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome, a pathway referred to as ER-associated protein degradation (ERAD). ERAD alleviates cytotoxic stress imposed by protein misfolding and is implicated in numerous diseases. ERAD is found in all eukaryotic cells but is best studied for the ERAD-L pathway in Saccharomyces cerevisiae, which disposes of misfolded glycoproteins in the ER lumen. The glycan attached to these proteins is first trimmed by glycosidases to generate a terminal α1,6-mannose residue. This residue, together with an unfolded polypeptide segment, targets the substrate to the Hrd1 complex, which is composed of the multispanning ubiquitin ligase Hrd1 and four additional proteins (Hrd3, Der1, Usa1, and Yos9). The Hrd1 complex mediates the retrotranslocation of the polypeptide into the cytosol, where it is polyubiquitinated, extracted from the membrane by the Cdc48 adenosine triphosphatase complex, and, finally, degraded by the proteasome.RATIONALEThe mechanism of ERAD-L remains poorly understood. Arguably the most mysterious aspect is how misfolded proteins cross the ER membrane, which normally presents a barrier to macromolecules. How ERAD-L substrates are recognized and distinguished from properly folding intermediates is also unclear. Answers to these questions require structural information on the Hrd1 complex.RESULTSHere, we report a structure of the active Hrd1 complex from S. cerevisiae, as determined by cryo–electron microscopy (cryo-EM) analysis of two subcomplexes. Our structures, biochemical data, and experiments in vivo indicate that the Hrd1 complex functions as a monomer in ERAD-L. Hrd3 and Yos9 jointly create a luminal binding site that recognizes misfolded glycoproteins. The α1,6-mannose residue binds to the mannose 6-phosphate receptor homology (MRH) domain of Yos9, and the polypeptide segment downstream of the glycan attachment site is likely accommodated in a groove of the luminal domain of Hrd3. Hrd1 and the rhomboid-like Der1 protein are linked by Usa1 on the cytosolic side of the membrane. Both Der1 and Hrd1 have lateral gates that face one another within the membrane and possess luminal and cytosolic cavities, respectively. Both proteins distort the membrane region between the lateral gates, making it much thinner than a normal phospholipid bilayer, an observation supported by molecular dynamics simulations. The structures and photocrosslinking experiments indicate that the retrotranslocation of an ERAD-L substrate is initiated by loop insertion of the polypeptide into the membrane, with one strand of the loop interacting with Der1 and the other with Hrd1.CONCLUSIONOur results lead to a model for the mechanism of retrotranslocation through the Hrd1 complex. The pathway across the membrane is formed by two “half-channels” corresponding to the luminal and cytosolic cavities of Der1 and Hrd1, respectively. These half-channels are juxtaposed in a thinned membrane region. The substrate inserts into the retrotranslocon as a hairpin that is hydrophilic on both sides. These features contrast with the Sec61 channel, which accepts substrates with a hydrophobic signal or transmembrane segment forming one side of the loop. This segment exits the lateral gate into the lipid environment and is not translocated, while the other side of the loop moves through the membrane in an entirely hydrophilic environment. The structural features of the retrotranslocon can facilitate movement of a fully hydrophilic substrate through a thinned and thus distorted membrane, a paradigm that may be replicated in other protein translocation systems.Initiation of ERAD-L revealed by cryo-EM and photocrosslinking.(A) Side view of a space-filling model of the Hrd1 complex, based on structures of the Hrd1 Usa1-Der1-Hrd3 and Hrd3-Yos9 subcomplexes. (B) Hypothetical position of a glycosylated ERAD-L substrate in the Hrd1 complex (dashed blue line). Substrate-interacting amino acid residues in Hrd1 and Der1 (red and orange, respectively) were determined by photocrosslinking. N, N terminus; C, C terminus; DHFR, dihydrofolate reductase; TM, transmembrane helix. (C) Model for the first three stages of retrotranslocation.Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo–electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two “half-channels” with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane.
Sandeep K Singh, Miao Gui, Fujiet Koh, Matthew CJ Yip, and Alan Brown. 2020. “Structure and activation mechanism of the BBSome membrane protein trafficking complex.” Edited by Andrew P Carter. eLife, 9, Pp. e53322. Publisher's VersionAbstract
Bardet-Biedl syndrome (BBS) is a currently incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS assemble into the BBSome, a key regulator of the ciliary membrane proteome. We report the electron cryomicroscopy (cryo-EM) structures of the native bovine BBSome in inactive and active states at 3.1 ­and 3.5 Å resolution, respectively. In the active state, the BBSome is bound to an Arf-family GTPase (ARL6/BBS3) that recruits the BBSome to ciliary membranes. ARL6 recognizes a composite binding site formed by BBS1 and BBS7 that is occluded in the inactive state. Activation requires an unexpected swiveling of the b-propeller domain of BBS1, the subunit most frequently implicated in substrate recognition, which widens a central cavity of the BBSome. Structural mapping of disease-causing mutations suggests that pathogenesis results from folding defects and the disruption of autoinhibition and activation.
Brianna Lowey, Aaron T. Whiteley, Alexander F. A. Keszei, Benjamin R. Morehouse, Ian T. Mathews, Sadie P. Antine, Victor J. Cabrera, Dmitry Kashin, Percy Niemann, Mohit Jain, Frank Schwede, John J. Mekalanos, Sichen Shao, Amy S.Y. Lee, and Philip J. Kranzusch. 2020. “CBASS Immunity Uses CARF-Related Effectors to Sense 3′–5′- and 2′–5′-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection.” Cell, 182, 1, Pp. 38-49.e17. Publisher's VersionAbstract
Summary cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzymes are immune sensors that synthesize nucleotide second messengers and initiate antiviral responses in bacterial and animal cells. Here, we discover Enterobacter cloacae CD-NTase-associated protein 4 (Cap4) as a founding member of a diverse family of >2,000 bacterial receptors that respond to CD-NTase signals. Structures of Cap4 reveal a promiscuous DNA endonuclease domain activated through ligand-induced oligomerization. Oligonucleotide recognition occurs through an appended SAVED domain that is an unexpected fusion of two CRISPR-associated Rossman fold (CARF) subunits co-opted from type III CRISPR immunity. Like a lock and key, SAVED effectors exquisitely discriminate 2′–5′- and 3′–5′-linked bacterial cyclic oligonucleotide signals and enable specific recognition of at least 180 potential nucleotide second messenger species. Our results reveal SAVED CARF family proteins as major nucleotide second messenger receptors in CBASS and CRISPR immune defense and extend the importance of linkage specificity beyond mammalian cGAS-STING signaling.
Benjamin R. Morehouse, Apurva A. Govande, Adi Millman, Alexander F. A. Keszei, Brianna Lowey, Gal Ofir, Sichen Shao, Rotem Sorek, and Philip J. Kranzusch. 2020. “STING cyclic dinucleotide sensing originated in bacteria.” Nature, 586, 7829, Pp. 429-433. Publisher's VersionAbstract
Stimulator of interferon genes (STING) is a receptor in human cells that senses foreign cyclic dinucleotides that are released during bacterial infection and in endogenous cyclic GMP–AMP signalling during viral infection and anti-tumour immunity1–5. STING shares no structural homology with other known signalling proteins6–9, which has limited attempts at functional analysis and prevented explanation of the origin of cyclic dinucleotide signalling in mammalian innate immunity. Here we reveal functional STING homologues encoded within prokaryotic defence islands, as well as a conserved mechanism of signal activation. Crystal structures of bacterial STING define a minimal homodimeric scaffold that selectively responds to cyclic di-GMP synthesized by a neighbouring cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzyme. Bacterial STING domains couple the recognition of cyclic dinucleotides with the formation of protein filaments to drive oligomerization of TIR effector domains and rapid NAD+ cleavage. We reconstruct the evolutionary events that followed the acquisition of STING into metazoan innate immunity, and determine the structure of a full-length TIR–STING fusion from the Pacific oyster Crassostrea gigas. Comparative structural analysis demonstrates how metazoan-specific additions to the core STING scaffold enabled a switch from direct effector function to regulation of antiviral transcription. Together, our results explain the mechanism of STING-dependent signalling and reveal the conservation of a functional cGAS–STING pathway in prokaryotic defence against bacteriophages.
Joshua A. Horwitz, Simon Jenni, Stephen C. Harrison, and Sean P. J. Whelan. 2020. “Structure of a rabies virus polymerase complex from electron cryo-microscopy.” Proceedings of the National Academy of Sciences, 117, 4, Pp. 2099–2107. Publisher's VersionAbstract
Rabies virus (RABV) and other viruses with single-segment, negative-sense, RNA genomes have a multi-functional polymerase protein (L) that carries out the various reactions required for transcription and replication. Many of these viruses are serious human pathogens, and L is a potential target for antiviral therapeutics. Drugs that inhibit polymerases of HCV and HIV-1 provide successful precedents. The structure described here of the RABV L protein in complex with its P-protein cofactor shows a conformation poised for initiation of transcription or replication. Channels in the molecule and the relative positions of catalytic sites suggest that L couples a distinctive capping reaction with priming and initiation of transcription, and that replication and transcription have different priming configurations and different product exit sites.Nonsegmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS RNA viruses carry all of the enzymatic functions required for viral messenger RNA (mRNA) transcription and replication: RNA polymerization, mRNA capping, and cap methylation. We describe here a complete structure of RABV L bound with its phosphoprotein cofactor (P), determined by electron cryo-microscopy at 3.3 Å resolution. The complex closely resembles the vesicular stomatitis virus (VSV) L-P, the one other known full-length NNS-RNA L-protein structure, with key local differences (e.g., in L-P interactions). Like the VSV L-P structure, the RABV complex analyzed here represents a preinitiation conformation. Comparison with the likely elongation state, seen in two structures of pneumovirus L-P complexes, suggests differences between priming/initiation and elongation complexes. Analysis of internal cavities within RABV L suggests distinct template and product entry and exit pathways during transcription and replication.
Eun Young Park, Shaun Rawson, Kunhua Li, Byeong-Won Kim, Scott B. Ficarro, Gonzalo Gonzalez-Del Pino, Humayun Sharif, Jarrod A. Marto, Hyesung Jeon, and Michael J. Eck. 2019. “Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes.” Nature. Publisher's VersionAbstract
RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1-3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4-6. At present, the structural basis of RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo-electron microscopy (cryo-EM). A 4.1?\AA resolution cryo-EM reconstruction reveals an inactive BRAF-MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.
Stephen M Hinshaw, Andrew N Dates, and Stephen C Harrison. 2019. “The structure of the yeast Ctf3 complex.” Edited by Andrea Musacchio. eLife, 8, Pp. e48215. Publisher's VersionAbstract
Kinetochores are the chromosomal attachment points for spindle microtubules. They are also signaling hubs that control major cell cycle transitions and coordinate chromosome folding. Most well-studied eukaryotes rely on a conserved set of factors, which are divided among two loosely-defined groups, for these functions. Outer kinetochore proteins contact microtubules or regulate this contact directly. Inner kinetochore proteins designate the kinetochore assembly site by recognizing a specialized nucleosome containing the H3 variant Cse4/CENP-A. We previously determined the structure, resolved by cryo-electron microscopy (cryo-EM), of the yeast Ctf19 complex (Ctf19c, homologous to the vertebrate CCAN), providing a high-resolution view of inner kinetochore architecture (Hinshaw and Harrison, 2019). We now extend these observations by reporting a near-atomic model of the Ctf3 complex, the outermost Ctf19c sub-assembly seen in our original cryo-EM density. The model is sufficiently well-determined by the new data to enable molecular interpretation of Ctf3 recruitment and function.
Edward C. Twomey, Zhejian Ji, Thomas E. Wales, Nicholas O. Bodnar, Scott B. Ficarro, Jarrod A. Marto, John R. Engen, and Tom A. Rapoport. 2019. “Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.” Science. Publisher's VersionAbstract
The Cdc48 ATPase (p97 or VCP in mammals) and its cofactor Ufd1/Npl4 extract poly-ubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-EM structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and poly-ubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.
Chao Fan, Minrui Fan, Benjamin J. Orlando, Nathan M. Fastman, Jinru Zhang, Yan Xu, Melissa G. Chambers, Xiaofang Xu, Kay Perry, Maofu Liao, and Liang Feng. 7/11/2018. “X-ray and cryo-EM structures of the mitochondrial calcium uniporter.” Nature, 559, Pp. 575-579.
Yibei Xiao, Min Luo, Adam E. Dolan, Maofu Liao, and Ailong Ke. 7/6/2018. “Structure basis for RNA-guided DNA degradation by Cascade and Cas3.” Science, 361, 6397.
Anura P. Srivastava, Min Luo, Wenchang Zhou, Jindrich Symersky, Dongyang Bai, Melissa G. Chambers, Jose D. Faraldo-Gomez, Maofu Liao, and David M. Mueller. 5/11/2018. “High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane.” Science, 360, 6389.
Wei Mi, Yanyan Li, Sung Hwan Yoon, Robert K. Ernst, Thomas Walz, and Maofu Liao. 9/14/2017. “Structural basis of MsbA-mediated lipopolysaccharide transport.” Nature, 549, Pp. 233-237.
Bart Alewijnse, Alun W. Ashton, Melissa G. Chambers, Songye Chen, Anchi Cheng, Mark Ebrahim, Edward T. Eng, Win J.H. Hagen, Abraham J. Koster, Claudia S. Lopez, Natalya Lukoyanova, Joaquin Ortega, Ludovic Renault, Steve Reyntjens, William J. Rice, Giovanna Scapin, Raymond Schrijver, Alistair Siebert, Scott M. Stagg, Valerie Grum-Tokars, Elizabeth R. Wright, Shenping Wu, Zhiheng Yu, Hong Zhou, Bridget Carragher, and Clinton S. Potter. 9/2017. “Best practices for managing large CryoEM facilities.” Journal of Structural Biology, 199, 3, Pp. 225-236.
Yibei Xiao, Min Luo, Robert B. Hayes, Jonathan Kim, Sherwin Ng, Fang Ding, Maofu Liao, and Ailong Ke. 6/29/2017. “Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.” Cell, 170, 1, Pp. 48-60.
Heng Ru, Melissa G. Chambers, Tian-Min Fu, Alexander B. Tong, Maofu Liao, and Hao Wu. 11/5/2015. “Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.” Cell, 163, 5, Pp. 1138-1152.