Publications

These 41 publications have resulted from work performed at the Stanford-SLAC CryoEM Center (S2C2), which is supported by the National Institutes of Health Common Fund Transformative High-Resolution Cryo-Electron Microscopy Program.

2022

Li, S.; Palo, M.Z.; Pintilie, G.; Zhang, X.; Su, Z.; Kappel, K.; Chiu, W.; Zhang, K.; Das, R. Topological crossing in the misfolded tetrahymena ribozyme resolved by cryo-EM. Proc national Acad Sci. 2022, 119, e2209146119. https//doi.org/10.1073/pnas.2209146119
Li, F.; Eriksen, J.; Oses-Prieto, J.A.; Gomez, Y.K.; Xu, H.; Finer-Moore, J.; Nguyen, P.; Bowen, A.; Nelson, A.; Burlingame, A.; Grabe, M.; Stroud, R.M.; Edwards, R.H. Allosteric Regulation of a Synaptic Vesicle Glutamate Transporter. BioRxiv2022, 2022.07.26.501550. https://doi.org/10.1101/2022.07.26.501550 (preprint)
Khant, H.; Li, Y. T.; Shankar, M.; Hecksel, C.; Mitchell, P.; Liu, Y.; Joubert, L.-M.; Zhang, C.; Dunn, L.; Schmid, M.; Hedman, B.; Chiu, W. Cryo-EM Information Management System and Sample Evaluation at Stanford-SLAC Cryo-EM Center. Microsc Microanal 2022, 28 (S1), 1304–1305. https://doi.org/10.1017/s1431927622005359 
Abskharon, R.; Sawaya, M. R.; Boyer, D. R.; Cao, Q.; Nguyen, B. A.; Cascio, D.; Eisenberg, D. S. Cryo-EM Structure of RNA-Induced Tau Fibrils Reveals a Small C-Terminal Core That May Nucleate Fibril Formation. Proc National Acad Sci 2022, 119 (15), e2119952119. https://doi.org/10.1073/pnas.2119952119 
Zhou, W.; Bammes, B.; Mitchell, P. G.; Betz, K.; Chiu, W. Electron Crystallography of Chiral and Non-Chiral Small Molecules. Ultramicroscopy 2022, 232, 113417. https://doi.org/10.1016/j.ultramic.2021.113417 
Fan, C.; Rees, D. C. Glutathione Binding to the Plant AtAtm3 Transporter and Implications for the Conformational Coupling of ABC Transporters. Elife 2022, 11, e76140. https://doi.org/10.7554/elife.76140 
Yu, Z.; Chen, J.; Takagi, E.; Wang, F.; Saha, B.; Liu, X.; Joubert, L.-M.; Gleason, C. E.; Jin, M.; Li, C.; Nowotny, C.; Agard, D.; Cheng, Y.; Pearce, D. Interactions between MTORC2 Core Subunits Rictor and MSin1 Dictate Selective and Context-Dependent Phosphorylation of Substrate Kinases SGK1 and Akt. J Biol Chem 2022, 102288. https://doi.org/10.1016/j.jbc.2022.102288 
Kafai, N. M.; Williamson, L. E.; Binshtein, E.; Sukupolvi-Petty, S.; Gardner, C. L.; Liu, J.; Mackin, S.; Kim, A. S.; Kose, N.; Carnahan, R. H.; Jung, A.; Droit, L.; Reed, D. S.; Handley, S. A.; Klimstra, W. B.; Crowe, J. E.; Diamond, M. S. Neutralizing Antibodies Protect Mice against Venezuelan Equine Encephalitis Virus Aerosol Challenge. J Exp Med 2022, 219 (4), e20212532. https://doi.org/10.1084/jem.20212532 
Yelshanskaya, M. V.; Patel, D. S.; Kottke, C. M.; Kurnikova, M. G.; Sobolevsky, A. I. Opening of Glutamate Receptor Channel to Subconductance Levels. Nature 2022, 605 (7908), 172–178. https://doi.org/10.1038/s41586-022-04637-w 
Koo, C. W.; Tucci, F. J.; He, Y.; Rosenzweig, A. C. Recovery of Particulate Methane Monooxygenase Structure and Activity in a Lipid Bilayer. Science 2022, 375 (6586), 1287–1291. https://doi.org/10.1126/science.abm3282 
Harris, J. A.; Faust, B.; Gondin, A. B.; Dämgen, M. A.; Suomivuori, C.-M.; Veldhuis, N. A.; Cheng, Y.; Dror, R. O.; Thal, D. M.; Manglik, A. Selective G Protein Signaling Driven by Substance P–Neurokinin Receptor Dynamics. Nat Chem Biol 2022, 18 (1), 109–115. https://doi.org/10.1038/s41589-021-00890-8 
Tsai, K.; Stojković, V.; Lee, D. J.; Young, I. D.; Szal, T.; Klepacki, D.; Vázquez-Laslop, N.; Mankin, A. S.; Fraser, J. S.; Fujimori, D. G. Structural Basis for Context-Specific Inhibition of Translation by Oxazolidinone Antibiotics. Nat Struct Mol Biol 2022, 29 (2), 162–171. https://doi.org/10.1038/s41594-022-00723-9 
Yang, K.; Wang, C.; White, K. I.; Pfuetzner, R. A.; Esquivies, L.; Brunger, A. T. Structural Conservation among Variants of the SARS-CoV-2 Spike Postfusion Bundle. Proc National Acad Sci 2022, 119 (16), e2119467119. https://doi.org/10.1073/pnas.2119467119 
Jiang, M.; Shin, J.; Simeon, R.; Chang, J.-Y.; Meng, R.; Wang, Y.; Shinde, O.; Li, P.; Chen, Z.; Zhang, J. Structural Dynamics of Receptor Recognition and PH-Induced Dissociation of Full-Length Clostridioides Difficile Toxin B. Plos Biol 2022, 20 (3), e3001589. https://doi.org/10.1371/journal.pbio.3001589 
Nguyen, B. A.; Afrin, S.; Singh, V.; Ahmed, Y.; Pedretti, R.; Fernandez-Ramirez, M. D. C.; Benson, M. D.; Sawaya, R. M.; Cao, Q.; Boyer, D.; Pope, A.; Wydorski, P. M.; Chhapra, F.; Eisenberg, D. S.; Saelices, L. Structural Polymorphism of Amyloid Fibrils in Cardiac ATTR Amyloidosis Revealed by Cryo-Electron Microscopy. BioRxiv 2022, 2022.06.21.496949. https://doi.org/10.1101/2022.06.21.496949 (preprint)
Fontana, P.; Dong, Y.; Pi, X.; Tong, A. B.; Hecksel, C. W.; Wang, L.; Fu, T.-M.; Bustamante, C.; Wu, H. Structure of Cytoplasmic Ring of Nuclear Pore Complex by Integrative Cryo-EM and AlphaFold. Science 2022, 376 (6598), eabm9326. https://doi.org/10.1126/science.abm9326 
Smith, E. M.; Ferrell, S.; Tokars, V. L.; Mondragón, A. Structures of an Active Type III-A CRISPR Effector Complex. Structure 2022, 30 (8), 1109-1128.e6. https://doi.org/10.1016/j.str.2022.05.013 
Rutledge, H. L.; Cook, B. D.; Nguyen, H. P. M.; HerzikJr., M. A.; Tezcan, F. A. Structures of the Nitrogenase Complex Prepared under Catalytic Turnover Conditions. Science 2022, eabq7641. https://doi.org/10.1126/science.abq7641 
Kim, D. S.; Watkins, A.; Bidstrup, E.; Lee, J.; Topkar, V.; Kofman, C.; Schwarz, K. J.; Liu, Y.; Pintilie, G.; Roney, E.; Das, R.; Jewett, M. C. Three-Dimensional Structure-Guided Evolution of a Ribosome with Tethered Subunits. Nat Chem Biol 2022, 1–9. https://doi.org/10.1038/s41589-022-01064-w 

 

2021

Powell, A. E.; Zhang, K.; Sanyal, M.; Tang, S.; Weidenbacher, P. A.; Li, S.; Pham, T. D.; Pak, J. E.; Chiu, W.; Kim, P. S. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS Central Sci 2021, 7 (1), 183–199. https://doi.org/10.1021/acscentsci.0c01405 
Eriksen, J.; Li, F.; Stroud, R. M.; Edwards, R. H. Allosteric Inhibition of a Vesicular Glutamate Transporter by an Isoform-Specific Antibody. Biochemistry-us 2021, 60 (32), 2463–2470. https://doi.org/10.1021/acs.biochem.1c00375 
Zimanyi, C. M.; Kopylov, M.; Potter, C. S.; Carragher, B.; Eng, E. T. Broadening Access to CryoEM through Centralized Facilities. Trends Biochem Sci 2021, 47 (2), 106–116. https://doi.org/10.1016/j.tibs.2021.10.007 
Zhang, K.; Zheludev, I. N.; Hagey, R. J.; Haslecker, R.; Hou, Y. J.; Kretsch, R.; Pintilie, G. D.; Rangan, R.; Kladwang, W.; Li, S.; Wu, M. T.-P.; Pham, E. A.; Bernardin-Souibgui, C.; Baric, R. S.; Sheahan, T. P.; D’Souza, V.; Glenn, J. S.; Chiu, W.; Das, R. Cryo-EM and Antisense Targeting of the 28-KDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome. Nat Struct Mol Biol 2021, 28 (9), 747–754. https://doi.org/10.1038/s41594-021-00653-y 
Sheedlo, M. J.; Durie, C. L.; Chung, J. M.; Chang, L.; Roberts, J.; Swanson, M.; Lacy, D. B.; Ohi, M. D. Cryo-EM Reveals New Species-Specific Proteins and Symmetry Elements in the Legionella Pneumophila Dot/Icm T4SS. Elife 2021, 10, e70427. https://doi.org/10.7554/elife.70427 
Hecksel, C.; Zhang, K.; Pintilie, G.; Mitchell, P.; Li, Y.-T.; Chiu, W. High Resolution Data Collection at S2C2, a National CryoEM Center. Microsc Microanal 2021, 27 (S1), 1152–1154. https://doi.org/10.1017/s1431927621004359 
Horikoshi, N.; Hwang, S.; Gati, C.; Matsui, T.; Castillo-Orellana, C.; Raub, A. G.; Garcia, A. A.; Jabbarpour, F.; Batyuk, A.; Broweleit, J.; Xiang, X.; Chiang, A.; Broweleit, R.; Vöhringer-Martinez, E.; Mochly-Rosen, D.; Wakatsuki, S. Long-Range Structural Defects by Pathogenic Mutations in Most Severe Glucose-6-Phosphate Dehydrogenase Deficiency. Proc National Acad Sci 2021, 118 (4), e2022790118. https://doi.org/10.1073/pnas.2022790118 
Cogan, D. P.; Zhang, K.; Li, X.; Li, S.; Pintilie, G. D.; Roh, S.-H.; Craik, C. S.; Chiu, W.; Khosla, C. Mapping the Catalytic Conformations of an Assembly-Line Polyketide Synthase Module. Science 2021, 374 (6568), 729–734. https://doi.org/10.1126/science.abi8358 
Hu, W.; Parkinson, C.; Zheng, H. Mechanistic Insights Revealed by YbtPQ in the Occluded State. BioRxiv 2021, 2021.06.15.448544. https://doi.org/10.1101/2021.06.15.448544 (preprint)
Neuberger, A.; Nadezhdin, K. D.; Sobolevsky, A. I. Structural Mechanisms of TRPV6 Inhibition by Ruthenium Red and Econazole. Nat Commun 2021, 12 (1), 6284. https://doi.org/10.1038/s41467-021-26608-x 
Klykov, O.; Gangwar, S. P.; Yelshanskaya, M. V.; Yen, L.; Sobolevsky, A. I. Structure and Desensitization of AMPA Receptor Complexes with Type II TARP Γ5 and GSG1L. Mol Cell 2021, 81 (23), 4771-4783.e7. https://doi.org/10.1016/j.molcel.2021.09.030 
He, Y.; Wang, Y.; Liu, B.; Helmling, C.; Sušac, L.; Cheng, R.; Zhou, Z. H.; Feigon, J. Structures of Telomerase at Several Steps of Telomere Repeat Synthesis. Nature 2021, 593 (7859), 454–459. https://doi.org/10.1038/s41586-021-03529-9.

 

2020

Zhang, K.; Li, S.; Pintilie, G.; Chmielewski, D.; Schmid, M. F.; Simmons, G.; Jin, J.; Chiu, W. A 3.4-Å Cryo-Electron Microscopy Structure of the Human Coronavirus Spike Trimer Computationally Derived from Vitrified NL63 Virus Particles. Qrb Discov 2020, 1, e11. https://doi.org/10.1017/qrd.2020.16
Fan, C.; Kaiser, J. T.; Rees, D. C. A Structural Framework for Unidirectional Transport by a Bacterial ABC Exporter. Proc National Acad Sci 2020, 117 (32), 19228–19236. https://doi.org/10.1073/pnas.2006526117
Roh, S.-H.; Shekhar, M.; Pintilie, G.; Chipot, C.; Wilkens, S.; Singharoy, A.; Chiu, W. Cryo-EM and MD Infer Water-Mediated Proton Transport and Autoinhibition Mechanisms of Vo Complex. Sci Adv 2020, 6 (41), eabb9605. https://doi.org/10.1126/sciadv.abb9605 
Partin, A. C.; Zhang, K.; Jeong, B.-C.; Herrell, E.; Li, S.; Chiu, W.; Nam, Y. Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA. Mol Cell 2020, 78 (3), 411-422.e4. https://doi.org/10.1016/j.molcel.2020.02.016 
Kumar, A.; Basak, S.; Rao, S.; Gicheru, Y.; Mayer, M. L.; Sansom, M. S. P.; Chakrapani, S. Mechanisms of Activation and Desensitization of Full-Length Glycine Receptor in Lipid Nanodiscs. Nat Commun 2020, 11 (1), 3752. https://doi.org/10.1038/s41467-020-17364-5 
Zhang, K.; Pintilie, G. D.; Li, S.; Schmid, M. F.; Chiu, W. Resolving Individual Atoms of Protein Complex by Cryo-Electron Microscopy. Cell Res 2020, 30 (12), 1136–1139. https://doi.org/10.1038/s41422-020-00432-2 
Chiu, W. Stanford-SLAC Cryo-EM Center. Acta Crystal 2020, 76 (a1), a200–a200. https://doi.org/10.1107/s0108767320098025 
Fromm, S. A.; Lawrence, R. E.; Hurley, J. H. Structural Mechanism for Amino Acid-Dependent Rag GTPase Nucleotide State Switching by SLC38A9. Nat Struct Mol Biol 2020, 27 (11), 1017–1023. https://doi.org/10.1038/s41594-020-0490-9 

 

2019

Chiu, W.; Li, Y. T.; Bushnell, D.; Schmid, M. F.; Skiniotis, G.; Hedman, B. Stanford-SLAC Cryo-EM Center (S2C2). Microsc Microanal 2019, 25 (S2), 2658–2659. https://doi.org/10.1017/s1431927619014028
Buffalo, C. Z.; Stürzel, C. M.; Heusinger, E.; Kmiec, D.; Kirchhoff, F.; Hurley, J. H.; Ren, X. Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission. Cell Host Microbe 2019, 26 (3), 359-368.e8. https://doi.org/10.1016/j.chom.2019.08.002​

 

 

 

Last Updated

Wed, 11/16/2022 - 13:36