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Applying 3D ED/MicroED workflows toward the next frontiers

Aragon, Mahira; Bowman, Sarah E J; Chen, Chun Hsing; de la Cruz, M Jason; Decato, Daniel A; Eng, Edward T; Flatt, Kristen M; Gulati, Sahil; Li, Yuchen; Lomba, Charles J; Mercado, Brandon; Miller, Jessalyn; Palatinus, Lukáš; Rice, William J; Waterman, David; Zimanyi, Christina M
We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.
PMID: 38712546
ISSN: 2053-2296
CID: 5664772

Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1

Thomas, Jonathan F; Valencia-Sánchez, Marco Igor; Tamburri, Simone; Gloor, Susan L; Rustichelli, Samantha; Godínez-López, Victoria; De Ioannes, Pablo; Lee, Rachel; Abini-Agbomson, Stephen; Gretarsson, Kristjan; Burg, Jonathan M; Hickman, Allison R; Sun, Lu; Gopinath, Saarang; Taylor, Hailey F; Sun, Zu-Wen; Ezell, Ryan J; Vaidya, Anup; Meiners, Matthew J; Cheek, Marcus A; Rice, William J; Svetlov, Vladimir; Nudler, Evgeny; Lu, Chao; Keogh, Michael-Christopher; Pasini, Diego; Armache, Karim-Jean
Histone H2A lysine 119 (H2AK119Ub) is monoubiquitinated by Polycomb repressive complex 1 and deubiquitinated by Polycomb repressive deubiquitinase complex (PR-DUB). PR-DUB cleaves H2AK119Ub to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. The PR-DUB subunits (BAP1 and ASXL1) are among the most frequently mutated epigenetic factors in human cancers. How PR-DUB establishes specificity for H2AK119Ub over other nucleosomal ubiquitination sites and how disease-associated mutations of the enzyme affect activity are unclear. Here, we determine a cryo-EM structure of human BAP1 and the ASXL1 DEUBAD in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for restructuring the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing insight into understanding cancer etiology.
PMID: 37556531
ISSN: 2375-2548
CID: 5594932

Measuring the Effect of Ice Thickness and Microscope Configuration on Resolution in Single Particle Cryo-EM

Chua, Eugene Y D; Neselu, Kasahun; Wang, Bing; Rice, William J; Potter, Clinton S; Carragher, Bridget
PMID: 37613233
ISSN: 1435-8115
CID: 5598692

CD19 CAR antigen engagement mechanisms and affinity tuning

He, Changhao; Mansilla-Soto, Jorge; Khanra, Nandish; Hamieh, Mohamad; Bustos, Victor; Paquette, Alice J; Garcia Angus, Andreina; Shore, Derek M; Rice, William J; Khelashvili, George; Sadelain, Michel; Meyerson, Joel R
Chimeric antigen receptor (CAR) T cell therapy relies on T cells that are guided by synthetic receptors to target and lyse cancer cells. CARs bind to cell surface antigens through an scFv (binder), the affinity of which is central to determining CAR T cell function and therapeutic success. CAR T cells targeting CD19 were the first to achieve marked clinical responses in patients with relapsed/refractory B cell malignancies and to be approved by the U.S. Food and Drug Administration (FDA). We report cryo-EM structures of CD19 antigen with the binder FMC63, which is used in four FDA-approved CAR T cell therapies (Kymriah, Yescarta, Tecartus, and Breyanzi), and the binder SJ25C1, which has also been used extensively in multiple clinical trials. We used these structures for molecular dynamics simulations, which guided creation of lower- or higher-affinity binders, and ultimately produced CAR T cells endowed with distinct tumor recognition sensitivities. The CAR T cells exhibited different antigen density requirements to trigger cytolysis and differed in their propensity to prompt trogocytosis upon contacting tumor cells. Our work shows how structural information can be applied to tune CAR T cell performance to specific target antigen densities.
PMID: 36867678
ISSN: 2470-9468
CID: 5432422

Measuring the effects of ice thickness on resolution in single particle cryo-EM

Neselu, Kasahun; Wang, Bing; Rice, William J.; Potter, Clinton S.; Carragher, Bridget; Chua, Eugene Y.D.
Ice thickness is a critical parameter in single particle cryo-EM "“ too thin ice can break during imaging or exclude the sample of interest, while ice that is too thick contributes to more inelastic scattering that precludes obtaining high resolution reconstructions. Here we present the practical effects of ice thickness on resolution, and the influence of energy filters, accelerating voltage, or detector mode. We collected apoferritin data with a wide range of ice thicknesses on three microscopes with different instrumentation and settings. We show that on a 300 kV microscope, using a 20 eV energy filter slit has a greater effect on improving resolution in thicker ice; that operating at 300 kV instead of 200 kV accelerating voltage provides significant resolution improvements at an ice thickness above 150 nm; and that on a 200 kV microscope using a detector operating in super resolution mode enables good reconstructions for up to 200 nm ice thickness, while collecting in counting instead of linear mode leads to improvements in resolution for ice of 50"“150 nm thickness. Our findings can serve as a guide for users seeking to optimize data collection or sample preparation routines for both single particle and in situ cryo-EM. We note that most in situ data collection is done on samples in a range of ice thickness above 150 nm so these results may be especially relevant to that community.
ISSN: 2590-1524
CID: 5424422

Smart data collection for CryoEM

Bepler, Tristan; Borst, Andrew J; Bouvette, Jonathan; Cannone, Giuseppe; Chen, Songye; Cheng, Anchi; Cheng, Ao; Fan, Quanfu; Grollios, Fanis; Gupta, Harshit; Gupta, Meghna; Humphreys, Theo; Kim, Paul T; Kuang, Huihui; Li, Yilai; Noble, Alex J; Punjani, Ali; Rice, William J; Oscar S Sorzano, Carlos; Stagg, Scott M; Strauss, Joshua; Yu, Lingbo; Carragher, Bridget; Potter, Clinton S
This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6-7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
PMID: 36341954
ISSN: 1095-8657
CID: 5357032

ACE2-containing defensosomes serve as decoys to inhibit SARS-CoV-2 infection

Ching, Krystal L; de Vries, Maren; Gago, Juan; Dancel-Manning, Kristen; Sall, Joseph; Rice, William J; Barnett, Clea; Khodadadi-Jamayran, Alireza; Tsirigos, Aristotelis; Liang, Feng-Xia; Thorpe, Lorna E; Shopsin, Bo; Segal, Leopoldo N; Dittmann, Meike; Torres, Victor J; Cadwell, Ken
Extracellular vesicles of endosomal origin, exosomes, mediate intercellular communication by transporting substrates with a variety of functions related to tissue homeostasis and disease. Their diagnostic and therapeutic potential has been recognized for diseases such as cancer in which signaling defects are prominent. However, it is unclear to what extent exosomes and their cargo inform the progression of infectious diseases. We recently defined a subset of exosomes termed defensosomes that are mobilized during bacterial infection in a manner dependent on autophagy proteins. Through incorporating protein receptors on their surface, defensosomes mediated host defense by binding and inhibiting pore-forming toxins secreted by bacterial pathogens. Given this capacity to serve as decoys that interfere with surface protein interactions, we investigated the role of defensosomes during infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of Coronavirus Disease 2019 (COVID-19). Consistent with a protective function, exosomes containing high levels of the viral receptor ACE2 in bronchoalveolar lavage fluid (BALF) from critically ill COVID-19 patients was associated with reduced intensive care unit (ICU) and hospitalization times. We found ACE2+ exosomes were induced by SARS-CoV-2 infection and activation of viral sensors in cell culture, which required the autophagy protein ATG16L1, defining these as defensosomes. We further demonstrate that ACE2+ defensosomes directly bind and block viral entry. These findings suggest that defensosomes may contribute to the antiviral response against SARS-CoV-2 and expand our knowledge on the regulation and effects of extracellular vesicles during infection.
PMID: 36099266
ISSN: 1545-7885
CID: 5335192

Structures of the T cell potassium channel Kv1.3 with immunoglobulin modulators

Selvakumar, Purushotham; Fernández-Mariño, Ana I; Khanra, Nandish; He, Changhao; Paquette, Alice J; Wang, Bing; Huang, Ruiqi; Smider, Vaughn V; Rice, William J; Swartz, Kenton J; Meyerson, Joel R
The Kv1.3 potassium channel is expressed abundantly on activated T cells and mediates the cellular immune response. This role has made the channel a target for therapeutic immunomodulation to block its activity and suppress T cell activation. Here, we report structures of human Kv1.3 alone, with a nanobody inhibitor, and with an antibody-toxin fusion blocker. Rather than block the channel directly, four copies of the nanobody bind the tetramer's voltage sensing domains and the pore domain to induce an inactive pore conformation. In contrast, the antibody-toxin fusion docks its toxin domain at the extracellular mouth of the channel to insert a critical lysine into the pore. The lysine stabilizes an active conformation of the pore yet blocks ion permeation. This study visualizes Kv1.3 pore dynamics, defines two distinct mechanisms to suppress Kv1.3 channel activity with exogenous inhibitors, and provides a framework to aid development of emerging T cell immunotherapies.
PMID: 35788586
ISSN: 2041-1723
CID: 5278332

The ups and downs of elevator-type di-/tricarboxylate membrane transporters

Sauer, David B; Wang, Bing; Sudar, Joseph C; Song, Jinmei; Marden, Jennifer; Rice, William J; Wang, Da-Neng
The divalent anion sodium symporter (DASS) family contains both sodium-driven anion cotransporters and anion/anion exchangers. The family belongs to a broader ion transporter superfamily (ITS), which comprises 24 families of transporters, including those of AbgT antibiotic efflux transporters. The human proteins in the DASS family play major physiological roles and are drug targets. We recently determined multiple structures of the human sodium-dependent citrate transporter (NaCT) and the succinate/dicarboxylate transporter from Lactobacillus acidophilus (LaINDY). Structures of both proteins show high degrees of structural similarity to the previously determined VcINDY fold. Conservation between these DASS protein structures and those from the AbgT family indicates that the VcINDY fold represents the overall protein structure for the entire ITS. The new structures of NaCT and LaINDY are captured in the inward- or outward-facing conformations, respectively. The domain arrangements in these structures agree with a rigid body elevator-type transport mechanism for substrate translocation across the membrane. Two separate NaCT structures in complex with a substrate or an inhibitor allowed us to explain the inhibition mechanism and propose a detailed classification scheme for grouping disease-causing mutations in the human protein. Structural understanding of multiple kinetic states of DASS proteins is a first step toward the detailed characterization of their entire transport cycle.
PMID: 34403567
ISSN: 1742-4658
CID: 5066842

One-pot synthesis of linear triblock terpolymers and their aqueous self-Assembly

Ahmed, Eman; Womble, C. Tyler; Cho, Jinwon; Dancel-Manning, Kristen; Rice, William J.; Jang, Seung Soon; Weck, Marcus
Compartmentalized micelles are prepared through the self-Assembly of linear triblock terpolymers containing hydrophilic (H), lipophilic (L), and fluorophilic (F) domains. The triblock copolymers were synthesized via living ring-opening metathesis polymerization (ROMP) of norbornene-based monomers. Our terpolymer design offers a facile approach for the synthesis of the target materials with fast polymerization kinetics, complete block incorporation and control over block sequence. Various triblock terpolymers are prepared with variations in block sequence and block ratio and self-Assembled in aqueous media. Interaction parameter (χ) values between each block are determined using a Flory-Huggins based computational model. "Core-shell-corona", "disk-like", "raspberry-like"and "worm-like"morphologies are observed through cryogenic transmission electron microscopy and dissipative particle dynamics simulations. This journal is
ISSN: 1759-9954
CID: 4860932