CSB Cryo-EM Publications

We expect the Principal Investigator and the User to acknowledge the CSB Cryo-EM Facility in research publications and presentations arising from their use of the facility. This acknowledgment should include the following or similar “EM data collections were conducted at the Center for Structural Biology Cryo-EM Facility at Vanderbilt University”.

Use of the Glacios should be specifically acknowledged with the following or similar: “We acknowledge the use of the Glacios cryo-TEM, which was acquired by NIH grant S10 OD030292-01”.

2024 Publications

• A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α–primase.  Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF. Nat Struct Mol Biol, March 2024.
• Structure of RADX and mechanism for regulation of RAD51 nucleofilaments.  Balakrishnan S, Adolph M, Tsai M, Akizuki T, Gallagher K, Cortez D, Chazin WJ. PNAS, February 2024.
• The open gate of the AMPA receptor forms a Ca²⁺ binding site critical in regulating ion transport.  Nakagawa T, Wang Xt, Miguez-Cabello FJ, Bowie D. Nat Struct Mol Biol, February 2024.

2023 Publications

• SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes. Wall SC, Suryadevara N, Kim C, Shiakolas AR, Holt CM, Irbe EB, Wasdin PT, Suresh YP, Binshtein E, Chen EC, Zost SJ, Canfield E, Crowe JE, Thompson-Arildsen M, Sheward DJ, Carnahan RH, Georgiev IS. Cell Reports Medicine, November 2023.
• Clostridioides difficile ferrosome organelles combat nutritional immunity.  Pi H, Sun R, McBride JR, Kruse ARS, Gibson-Corley KN, Krystofiak ES, Nicholson MR, Spraggins JM, Zhou Q, Skaar EP.  Nature, November 2023.
• Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Tang Q, Sinclair M, Hasdemir H, Stein R, Karakas E, Tajkhorshid E, Mchaourab H. Nature Comm, November 2023.
• Nanobodies against C. difficile TcdA and TcdB reveal unexpected neutralizing epitopes and provide a toolkit for toxin quantitation in vivo.  Kordus SL, Kroh HK, Rodríguez RC, Shrem RA, Peritore-Galve FC, Shupe JA, Wadzinski BE, Lacy DB, Spiller BW. PLOS Pathogens, October 2023.
• Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase.  Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Journal of Molecular Biology, October 2023.
• Multifunctional human monoclonal antibody combination mediates protection against Rift Valley fever virus at low doses.  Chapman NS, Hulswit RJG, Westover JLB, Stass R, Paesen GC, Binshtein E, Reidy JX, Engdahl TB, Handal LS, Flores A, Gowen BB, Bowden TA, Crowe JE Jr. Nature Communications, September 2023.
• Structures of the Insecticidal Toxin Complex Subunit XptA2 Highlight Roles for Flexible Domains. Martin CL, Chester DW, Radka CD, Pan L, Yang Z, Hart RC, Binshtein EM, Wang Z, Nagy L, DeLucas LJ, Aller SG.  International Journal of Molecular Sciences, August 2023.
• Role of the CagY antenna projection in Helicobacter pylori Cag type IV secretion system activity.  Tran SC, McClain MS, Cover TL.  Microbial Pathogenesis, August 2023.
• CryoEM structure of a post-assembly MS-ring reveals plasticity in stoichiometry and conformation.  Singh PK, Cecchini G, Nakagawa N, Iverson, TM. PLOS One, May 2023.
• Hybrid Shear-Thinning Hydrogel Integrating Hyaluronic Acid with ROS-Responsive Nanoparticles.  Bezold MG, Hanna AR, Dollinger BR, Patil P, Yu F, Duvall CL, Gupta MK.  Advanced Functional Materials, May 2023.
• Systematic analysis of human antibody response to ebolavirus glycoprotein shows high prevalence of neutralizing public clonotypes.  Chen EC, Gilchuk P, Zost SJ, Ilinykh PA, Binshtein E, Huang K, Myers L, Bonissone S, Day S, Kona CR, Trivette A, Reidy JX, Sutton RE, Gainza C, Diaz S, Williams JK, Selverian CN, Davidson E, Ollmann Saphire E, Doranz BJ, Castellana N, Bukreyev A, Carnahan RH, Crowe JE.  Cell Reports, April 2023.
• Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies.  Engdahl TB, Binshtein E, Brocato RL, Kuzmina NA, Principe LM, Kwilas SA, Kim RK, Chapman NS, Porter MS, Guardado-Calvo P, Rey FA, Handal LS, Diaz SM, Zagol-Ikapitte IA,Tran MH, McDonald WH, Meiler J, Reidy JX, Trivette A,  Bukreyev A, Hooper JW, Crowe JE. eLife, March 2023.
• Cryo-EM structures of a LRRC8 chimera with native functional properties reveal heptameric assembly.  Takahashi H, Yamada T, Denton JS, Strange K, Karakas E. eLife, March 2023.
• A mechanistic model of primer synthesis from catalytic structures of DNA polymerase α–primase.  Mullins EA, Salay LE, Durie CL, Jackman JE, Ohi MD, Chazin WJ, Eichman BF.  bioRxiv, March 2023.
• Functional HIV-1/HCV cross-reactive antibodies isolated from a chronically co-infected donor. Pilewski KA, Wall S, Richardson SI, Manamela NP, Clark K, Hermanus T, Binshtein E, Venkat R,  Sautto GA, Kramer KJ, Shiakolas AR, Setliff I, Salas J, Mapengo RE, Suryadevara N,  Brannon JP,  Beebout CJ, Parks R, Raju N, Frumento N, Walker LM, Fechter EF, Qin JS, Murji AA, Janowska K, Thakur B, Lindenberger J, May AJ, Huang X, Sammour S, Acharya P, Carnahan RH, Ross TM, Haynes BF, Hadjifrangiskou M, Crowe JE , Bailey JP, Kalams S, Morris L, Georgiev IS. Cell Reports, Feb 2023.

2022 Publications

• Structural insights into the mechanism of the sodium/iodide symporter.  Ravera S, Nicola JP, Salazar-De Simone G, Sigworth FJ, Karakas E, Amzel LM, Bianchet MA, Carrasco N. Nature, Dec 2022.
• Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants. Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Engdahl TB, Chen E, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JK, Rubinfeld B, Saada EA, Weisenberger T, Lee T, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Bates TW, Petersen BK, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Diamond MS, Crowe JE, Carnahan RH, Faissol DM. bioRxiv, Oct 2022.
• Improved mammalian retromer cryo-EM structures reveal a new assembly interface.  Kendall AK, Chandra M, Xie B, Wan W, Jackson LP. JBC, Sept 2022.
• Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies.  Engdahl TB, Binshtein E, Brocato RL, Kuzmina NA, Principe LM, Kwilas SA, Kim RK, Chapman NS, Porter MS, Guardado-Calvo P, Rey FA, Handal LS, Diaz SM, Zagol-Ikapitte IA, Reidy JX, Trivette A, Bukreyev A, Hooper JW, Crowe JE. bioRxiv, July 2022.
• Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region. Schoeder CT, Gilchuk P, Sangha AK, Ledwitch KV, Malherbe DC, Zhang X, Binshtein E, Williamson LE, Martina CE, Dong J, Armstrong E, Sutton R, Nargi R, Rodriguez J, Kuzmina N, Fiala B, King NP, Bukreyev A, Crowe JE, Meiler J. PLOS Pathogens, May 2022.
• An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer.  Suryadevara N, Shiakolas AR, VanBlargan LA, Binshtein E, Chen RE, Case JB, Kramer KJ, Armstrong EC, Myers L, Trivette A, Gainza C, Nargi RS, Selverian CN, Davidson E, Doranz BJ, Diaz SM, Handal LS, Carnahan RH, Diamond MS, Georgiev IS, Crowe JE. J Clin Invest, April 2022.
• Neutralizing antibodies protect mice against Venezuelan equine encephalitis virus aerosol challenge.  Kafai NM, Williamson LE, Binshtein E, Sukupolvi-Petty S, Gardner CL, Lui J, Mackin S, Kim AS, Kose N, Carnahan PH, Jung A, Droit L, Reed DS, Handley SA, Klimstra WB, Crowe JE, Diamond MS. J Exp Med, March 2022.
• Structural basis for activation and gating of IP3 receptors. Schmitz EA, Takahashi H, Karakas E. Nature Communications, March 2022.
• Systematic analysis of human antibody response to ebolavirus glycoprotein reveals high prevalence of neutralizing public clonotypes.  Chen EC, Gilchuk P, Zost SJ, Ilinykh PA, Binshtein E, Huang K, Myers L, Bonissone S, Day S, Kona CR, Trivette A, Reidy JX, Sutton RE, Gainza C, Monroig S, Davidson E, Saphire EO, Doranz BJ, Castellana N, Bukreyev A, Carnahan RH, Crowe JE.  bioRxiv, Jan 2022.

2021 Publications

• Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.  Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, Xie X, Zhang X, Shi P, Logue J, Weston S, McGrath ME, Frieman MB, Brady T, Tuffy KM, Bright H, Loo Y, McTamney PM, Esser MT, Carnahan RH, Diamond MS, Bloom JD, Crowe JE. Nature Microbiology, Oct 2021.
• Functional properties of oligomeric and monomeric forms of Helicobacter pylori VacA toxin.  Caso GC, McClain MS, Erwin AL, Truelock MD, Campbell AM, Leasure CS, Nagel M, Schey KL, Lacy DB, Ohi MD, Cover TL.  Infection and Immunity, Sept 2021.
• Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals.  Chen EC, Gilchuk P, Zost SJ, Suryadevara N, Winkler ES, Cabel CR, Binshtein E, Chen RS, Sutton RE, Rodriguez J, Day S, Meyers L, Trivette A, Williams JK, Davidson E, Li S, Doranz BJ, Campos SK, Crowe JE.  Cell Reports, Aug 2021.
• Cooperativity mediated by rationally selected combinations of human monoclonal antibodies targeting the heniparvirus receptor binding protein.  Doyle MP, Kose N, Borisevich V, Binshtein E, Amaya M, Nagel M, Annand EJ, Armsgtrong E, Mombardi R, Dong J, Schey KL, Broder CC, Zeitlin L, Kuang EA, Bornholdt ZA, West BR, Geisbert TW, Cross RW, Crowe JE. Cell Reports, Aug 2021.
• Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein.  Suryadevara N, Shrihari S, Gilchuk P, VanBlargan LA, Binshtein E, Zost SJ, Nargi RS, Sutton RE, Winkler ES, Chen ES, Fouch ME, Davidson E, Doranz BJ, Chen RE, Shi P, Carnahan RH, Thackray LB, Diamond MS, Crowe JE. Cell, Apr 2021.
• Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2.  Xie Y, Clarke BP, Kim YJ, Ivey AL, Hill PS, Shi Y, Ren Y. eLife, Mar 2021.
• RADX controls RAD51 filament dynamics to regulate replication fork stability. Adolph MB, Mohamed TM, Balakrishnan S, Xue C, Morati F, Modesti M, Greene EC, Chazin WJ, Cortez D. Molecular Cell, Mar 2021.
• Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE, Bloom JD. Cell Host & Microbe, Jan 2021.

2020 Publications

• Human antibodies protect against aerosolized Eastern equine encephalitis virus infection.  WIllaimson LE, Gilliand T, Yadav PK, Binshtein E, Bombardi R, Kose N, Nargi RS, Sutton RE, Durie CL, Armstrong E, Carnahan RH, Walker LM, Kim AS, Fox JM, Diamond MS, Ohi MD, Klimstra WB, Crowe JE.  Cell, Dec 2020.
• Structure and assembly of CAV1 8S complexes revealed by single particle electron microscopy. Han B, Porta JC, Hanks JL, Peskova Y, Binshtein E, Dryden K, Claxton DP, Mchaourab HS, Karakas E, Ohi MD, Kenworthy AK. Science Advances, Dec 2020.
• The host cell metabolite inositol hexakisphosphate promotes efficient endogenous HIV-1 reverse transcription by stabilizing the viral capsid. Jennings J, Shi J, Varadarajan J, Jamieson PJ, Aiken C. mBio, Dec 2020.
• Improved negative stain electron microscopy procedure for detecting surface detail on high density lipoproteins.  Hart, R. Microscopy Today, Sep 2020.
• Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein.  Zost SJ, Gilchuk P, Chen RE, Case JB, Reidy JX, Trivette A, Nargi RS, Sutton RE, Suryadevara N, Chen EC, Binshtein E, Shrihari S, Ostrowski M, Chu HY, Didier JE, MacRenaris KW, Jones T, Day S, Myers L, Lee FE, Nguyen DC, Sanz I, Martinez DR, Rothlaud PW, Bloyet L, Whelan SPJ, Baric RS, Thackray LB, Diamond MS, Carnahan RH, Crowe JE.  Nature Medicine, Sep 2020.
• Bicelles rich in both sphingolipids and cholesterol and their use in studies of membrane proteins.  Hutchison JM, Shih K, Scheidt HA, Fantin SM, Parson KF, Pantelopulos GA, Harrington HR, Mittendorf KF, Voehler MW, Ruotolo BT, Huster D, McFeeters RL, Straub JE, Nieh M, Sanders CR. JACS, July 2020.
• Potently neutralizing and protective human antibodies against SARS-CoV-2.  Zost SJ, Gilchuk P, Case JB, Binshtein E, Chen RE, Nkoloa JP, Schafer A, Reidy JX, Trivette A, Nargi RS, Sutton RE, Suryadevara N, Martinez DR, Williamson LE, Chen EC, Jones T, Day S, Myers L, Hassan AO, Kafai NM, Winkler ES, Fox JM, Shrihari S, Mueller BK, Meiler J, Chandrashekar A, Mercado NB, Steinhardt JJ, Ren K, Loo Y, Kallewaard NL, McCune BT, Keeler SP, Holzman MJ, Barouch DH, Gralinski LE, Baric RS, Thackray LB, Diamond MS, Carhahan RH, Crowe JE.  Nature, Jul 2020.
• Functional properties of Helicobacter pylori VacA toxin m1 and m2 variants. Caston RR, Sierra JC, Foegeding NJ, Truelock MD, Campbell AM, Frick-Cheng AE, Bimczok D, Wilson KT, McClain MS, Cover TL.  Infection and Immunity, Jun 2020.
• Structural elucidation of the Clostridioides difficle transferase toxin reveals a single-site binding mode for the enzyme.  Sheedlo MJ, Anderson DM, Thomas AK, Lacy DB. PNAS, Feb 2020.

  

• Mammalian retromer is an adaptable scaffold for cargo sorting from endosomes.  Kendall AK, Xie B, Xu P, Wang J, Burcham R, Frazier MN, Binshtein E, Wei H, Graham TR, Nakagawa T, Jackson LP.  Structure, Feb 2020.
• AMPA receptor structure and auxiliary subunits.  Kamalova A, Nakagawa T.  Journal of Physiology, Jan 2020.
• Cryo-EM structure of human type-3 inositol triphosphate receptor reveals the presence of a self-binding peptide that acts as an antagonist.  Azumaya CM, Linton EA, Risener CJ, Nakagawa T, Karakas E. Journal of Biological Chemistry, Jan 2020.

2019 Publications

• Structures of the AMPA receptor in complex with its auxiliary subunit cornichon.  Nakagawa T. Science, Dec 2019.
• Bacterial Energetic Requirements for Helicobacter pylori Cag TypeIV secretion system-dependent alterations in gastric epithelial cells.  Lin AS, Dooyema SDR, Frick-Cheng AE, Harvey ML, Suarez G, Loh JT, McDonald WH, McClain MS, Peek Jr RM, Cover TL.  Infection and Immunity, Nov 2019.
• Structural Insights into the Transition of Clostridioides difficile Binary Toxin from Prepore to Pore.  Anders DM, Sheedlo MJ, Jensen JL, Lacy DB. Nature Microbiology, Nov 2019.
• Dominant Negative MA-CA Fusion Protein is Incorporated into HIV-1 Cores and Inhibits Nuclear Entry of Viral Preintegration Complexes. Anderson-Daniels J, Singh PK, Sowd GA, Li W, Engelman AN, Aiken C. Journal of Virology, Nov 2019.

2018 Publications

• Structure-function analyses of the ion channel TRPC3 reveal that its cytoplasmic domain allosterically modulates channel gating.  Sierra-Valdez F, Azumaya CM, Romero LO, Nakagawa T, Cordero-Morales JF.  Journal of Biological Chemistry, Aug 2018.
• Multifunctional pan-ebolavirus antibody recognizes a site of broad vulnerability on the ebolavirus glycoprotein. Gilchuk P, Kuzmina N, Ilinykh PA, Huang K, Gunn BM, Bryan A, Davidson E, Doranz BJ, Turner HL, Fusco ML, Bramble MS, Hoff NA, Binshtein E, Kose N, Flyak AI, Flinko R, Orlandi C, Carnahan R, Parrish EH, Sevy AM, Bombardi RG, Singh PK, Mukadi P, Muyembe-Tamfum JJ, Ohi MD, Saphire EO, Lewis GK, Alter G, Ward AB, Rimoin AW, Bukreyev A, Crowe JE. Immunity, Jul 2018.
• Cryo-EM structure of the cytoplasmic domain of murine transient receptor potential cation channel subfamily C member 6 (TRPC6). Azumaya CM, Sierra-Valdez F, Cordero-Morales JF, Nakagawa T. Journal of Biological Chemistry, Jul 2018.
• Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins. Mousa JJ, Binshtein E, Human S, Fong RH, Alvarado G, Doranz BJ, Moore ML, Ohi MD, Crowe JE. PLoS Pathogens, Feb 2018.
• A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells. Kroh HK, Chandrasekaran R, Zhang Z, Rosenthal K, Woods R, Jin X, Nyborg AC, Rainey GJ, Warrener P, Melnyk RA, Spiller BW, Lacy DB. Journal of Biological Chemistry, Jan 2018.

2017 Publications

• Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface. Kroh HK, Chandrasekaran R, Rosenthal K, Woods R, Jin X, Ohi MD, Nyborg AC, Rainey GJ, Warrener P, Spiller BW, Lacy DB. Journal of Biological Chemistry, Sep 2017.
• Peripheral myelin protein 22 alters membrane architecture. Mittendorf KF, Marinko JT, Hampton CM, Ke Z, Hadziselimovic A, Schlebach JP, Law CL, Li J, Wright ER, Sanders CR, Ohi MD. Science Advances, Jul 2017.
• Epitopes and Mechanism of Action of the Clostridium difficile Toxin A-Neutralizing Anti8body Actoxumab. Hernandez LD, Kroh HK, Hsieh E, Yang X, Beaumont M, Sheth PR, DiNunzio E, Rutherford SA, Ohi MD, Ermakov G, Xiao L, Secore S, Karczewshi J, Racine F, Mayhood T, Fischer P, Sher X, Gupta P, Lacy DB, Therien AG. Journal of Molecular Biology, Apr 2017.
• While the revolution will not be crystallized, biochemistry reigns supreme. Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. Protein Science, Jan 2017.