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Instruments / Technical Area	Publication Details	Published
NONE-No attached Diamond beamline	Pathogen-sugar interactions revealed by universal saturation transfer analysis Charles J. Buchanan , Ben Gaunt , Peter J. Harrison , Yun Yang , Jiwei Liu , Aziz Khan , Andrew M. Giltrap , Audrey Le Bas , Philip N. Ward , Kapil Gupta , Maud Dumoux , Tiong Kit Tan , Lisa Schimaski , Sergio Daga , Nicola Picchiotti , Margherita Baldassarri , Elisa Benetti , Chiara Fallerini , Francesca Fava , Annarita Giliberti , Panagiotis I. Koukos , Matthew J. Davy , Abirami Lakshminarayanan , Xiaochao Xue , Georgios Papadakis , Lachlan P. Deimel , Virgínia Casablancas-Antràs , Timothy D. W. Claridge , Alexandre M. J. J. Bonvin , Quentin J. Sattentau , Simone Furini , Marco Gori , Jiandong Huo , Raymond J. Owens , Christiane Schaffitzel , Imre Berger , Alessandra Renieri , James H. Naismith , Andrew J. Baldwin , Benjamin G. Davis Science 479 DOI: 10.1126/science.abm3125 Open Access Show Abstract ▼ Abstract: Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily-modified pathogen proteins can be confounded by overlapping sugar signals and/or compound with known experimental constraints. ‘Universal saturation transfer analysis’ (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin lineage SARS-CoV-2 spike trimer binds sialoside sugars in an ‘end-on’ manner. uSTA-guided modelling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar-binding in SARS CoV 2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins in deeper human lung as potentially relevant to virulence and/or zoonosis.	Jun 2022
Krios I-Titan Krios I at Diamond	CryoEM structure of the super-constricted two-start dynamin 1 filament Jiwei Liu , Frances Joan D. Alvarez , Daniel K. Clare , Jeffrey K. Noel , Peijun Zhang Nature Communications 12 DOI: 10.1038/s41467-021-25741-x Diamond Proposal Number(s): [14393] Open Access Show Abstract ▼ Abstract: Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance.	Sep 2021
Krios I-Titan Krios I at Diamond	The molecular basis of regulation of bacterial capsule assembly by Wzc Yun Yang , Jiwei Liu , Bradley R. Clarke , Laura Seidel , Jani R. Bolla , Philip N. Ward , Peijun Zhang , Carol V. Robinson , Chris Whitfield , James Naismith Nature Communications 12 DOI: 10.1038/s41467-021-24652-1 Diamond Proposal Number(s): [20223] Open Access Show Abstract ▼ Abstract: Bacterial extracellular polysaccharides (EPSs) play critical roles in virulence. Many bacteria assemble EPSs via a multi-protein “Wzx-Wzy” system, involving glycan polymerization at the outer face of the cytoplasmic/inner membrane. Gram-negative species couple polymerization with translocation across the periplasm and outer membrane and the master regulator of the system is the tyrosine autokinase, Wzc. This near atomic cryo-EM structure of dephosphorylated Wzc from E. coli shows an octameric assembly with a large central cavity formed by transmembrane helices. The tyrosine autokinase domain forms the cytoplasm region, while the periplasmic region contains small folded motifs and helical bundles. The helical bundles are essential for function, most likely through interaction with the outer membrane translocon, Wza. Autophosphorylation of the tyrosine-rich C-terminus of Wzc results in disassembly of the octamer into multiply phosphorylated monomers. We propose that the cycling between phosphorylated monomer and dephosphorylated octamer regulates glycan polymerization and translocation.	Jul 2021
Krios I-Titan Krios I at Diamond	Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily Jiwei Liu , Matteo Tassinari , Diorge P. De Souza , Souvik Naskar , Jeffrey K. Noel , Olga Bohuszewicz , Martin Buck , Tom A. Williams , Buzz Baum , Harry H. Low Cell 184, 3660 - 3673.e18 DOI: 10.1016/j.cell.2021.05.041 Diamond Proposal Number(s): [16942] Open Access Show Abstract ▼ Abstract: Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.	Jul 2021
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond Krios III-Titan Krios III at Diamond	CryoET structures of immature HIV Gag reveal six-helix bundle Luiza Mendonca , Dapeng Sun , Jiying Ning , Jiwei Liu , Abhay Kotecha , Mateusz Olek , Thomas Frosio , Xiaofeng Fu , Benjamin A. Himes , Alex B. Kleinpeter , Eric O. Freed , Jing Zhou , Christopher Aiken , Peijun Zhang Communications Biology 4 DOI: 10.1038/s42003-021-01999-1 Diamond Proposal Number(s): [18477, 21005, 21004] Open Access Show Abstract ▼ Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.	Apr 2021
	The architecture of inactivated SARS-COV-2 with postfusion spikes revealed by cryo-EM and cryo-ET Chuang Liu , Luiza Mendonca , Yang Yang , Yuanzhu Gao , Chenguang Shen , Jiwei Liu , Tao Ni , Bin Ju , Congcong Liu , Xian Tang , Jinli Wei , Xiaomin Ma , Yanan Zhu , Weilong Liu , Shuman Xu , Yingxia Liu , Jing Yuan , Jing Wu , Zheng Liu , Zheng Zhang , Lei Li , Peiyi Wang , Peijun Zhang Structure DOI: 10.1016/j.str.2020.10.001 Open Access Show Abstract ▼ Abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) resulted from the outbreak of SARS-CoV-2 in December 2019. Currently, multiple efforts are being made to rapidly develop vaccines and treatments to fight COVID-19. Current vaccine candidates use inactivated SARS-CoV-2 viruses; therefore, it is important to understand the architecture of inactivated SARS-CoV-2. We have genetically and structurally characterized β-propiolactone-inactivated viruses from a propagated and purified clinical strain of SARS-CoV-2. We observed that the virus particles are roughly spherical or moderately pleiomorphic. Although a small fraction of prefusion spikes are found, most spikes appear nail shaped, thus resembling a postfusion state, where the S1 protein of the spike has disassociated from S2. Cryoelectron tomography and subtomogram averaging of these spikes yielded a density map that closely matches the overall structure of the SARS-CoV postfusion spike and its corresponding glycosylation site. Our findings have major implications for SARS-CoV-2 vaccine design, especially those using inactivated viruses.	Oct 2020
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond	Structural basis for membrane tethering by a bacterial dynamin-like pair Jiwei Liu , Jeffrey K. Noel , Harry H. Low Nature Communications 9 DOI: 10.1038/s41467-018-05523-8 Diamond Proposal Number(s): [15597] Open Access Show Abstract ▼ Abstract: Dynamin-like proteins (DLPs) are large GTPases that restructure membrane. DLPs such as the mitofusins form heterotypic oligomers between isoform pairs that bridge and fuse opposing membranes. In bacteria, heterotypic oligomerisation may also be important for membrane remodelling as most DLP genes are paired within operons. How DLPs tether opposing membranes is unknown. Here we show the crystal structure of a DLP heterotypic pair from the pathogen Campylobacter jejuni. A 2:2 stoichiometric tetramer is observed where heterodimers, conjoined by a random coil linker, assemble back-to-back to form a tripartite DLP chain with extreme flexibility. In vitro, tetramerisation triggers GTPase activity and induces lipid binding. Liposomes are readily tethered and form tubes at high tetramer concentration. Our results provide a direct mechanism for the long-range binding and bridging of opposing membranes by a bacterial DLP pair. They also provide broad mechanistic and structural insights that are relevant to other heterotypic DLP complexes.	Aug 2018

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