CryoEM Core Publications

Akey, Christopher W., Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M. Varberg, Zulin Yu, et al. 2022. “Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex.” Cell 185 (2): 361–78.e25. PMID: 34982960, PMCID: PMC8928745

Chen, Muyuan, Xiaodong Shi, Zhili Yu, Guizhen Fan, Irina I. Serysheva, Matthew L. Baker, Ben F. Luisi, Steven J. Ludtke, and Zhao Wang. 2022. “In Situ Structure of the AcrAB-TolC Efflux Pump at Subnanometer Resolution.” Structure  30 (1): 107–13.e3. PMID: 34506732, PMCID: PMC8741639

Chen M, Shi X, Yu Z, Fan G, Serysheva II, Baker ML, Luisi BF, Ludtke SJ, Wang Z. In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution. Structure. 2022 Jan 6;30(1):107-113.e3. doi: 10.1016/j.str.2021.08.008. Epub 2021 Sep 9. PMID: 34506732; PMCID: PMC8741639.

Hu L, Salmen W, Chen R, Zhou Y, Neill F, Crowe JE Jr, Atmar RL, Estes MK, Prasad BVV. Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity. Nat Commun. 2022 Mar 10;13(1):1241. doi: 10.1038/s41467-022-28757-z. PMID: 35273142; PMCID: PMC8913647.

Ettayebi K, Salmen W, Imai K, Hagi A, Neill FH, Atmar RL, Prasad BVV, Estes MK. Antiviral Activity of Olanexidine-Containing Hand Rub against Human Noroviruses. mBio. 2022 Apr 26;13(2):e0284821. doi: 10.1128/mbio.02848-21. Epub 2022 Mar 17. PMID: 35297675; PMCID: PMC9040745.

Chen, Muyuan, and Steven J. Ludtke. 2021. “Deep Learning-Based Mixed-Dimensional Gaussian Mixture Model for Characterizing Variability in Cryo-EM.” Nature Methods 18 (8): 930–36. PMID: 34326541, PMCID: PMC8363932

Potter, Valencia L., Abigail R. Moye, Michael A. Robichaux, and Theodore G. Wensel. 2021. “Super-Resolution Microscopy Reveals Photoreceptor-Specific Subciliary Location and Function of Ciliopathy-Associated Protein CEP290.” JCI Insight. PMID: 34050409, PMCID: PMC8564900

Wensel, Theodore G., Valencia L. Potter, Abigail Moye, Zhixian Zhang, and Michael A. Robichaux. 2021. “Structure and Dynamics of Photoreceptor Sensory Cilia.” Pflugers Archiv: European Journal of Physiology 473 (9): 1517–37. PMID: 34520396, PMCID: PMC8564900

Yu W, Singh R, Wang Z, O'Malley BW, Yi P. The E3 ligase TRAF4 promotes IGF signaling by mediating atypical ubiquitination of IRS-1. J Biol Chem. 2021 Jan-Jun;296:100739. doi: 10.1016/j.jbc.2021.100739. Epub 2021 May 13. PMID: 33991522; PMCID: PMC8191236.

Yi P, Yu X, Wang Z, O'Malley BW. Steroid receptor-coregulator transcriptional complexes: new insights from CryoEM. Essays Biochem. 2021 Dec 17;65(6):857-866. doi: 10.1042/EBC20210019. PMID: 34061186; PMCID: PMC8845409.

De Giorgi, Marco, Kelsey E. Jarrett, Jason C. Burton, Alexandria M. Doerfler, Ayrea Hurley, Ang Li, Rachel H. Hsu, et al. 2020. “Depletion of Essential Isoprenoids and ER Stress Induction Following Acute Liver-Specific Deletion of HMG-CoA Reductase.” Journal of Lipid Research 61 (12): 1675–86. PMID: 33109681, PMCID: PMC7707164

Dilip Kumar, Xinzhe Yu, Sue E. Crawford, Rodolfo Moreno, Joanita Jakana, Banumathi Sankaran, Ramakrishnan Anish, Soni Kaundal, Liya Hu, Mary K. Estes, Zhao Wang, B.V. Venkataram Prasad. 2.7 Å cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity, Science Advances 15 Apr 2020: EAAY6410

Yang Zeng*, Ren Ren*, Gundeep Kaur*, Swanand Hardikar, Zhengzhou Ying, Lance Babcock, Esha Gupta, Xing Zhang, Taiping Chen, Xiaodong Cheng. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes and Development. 2020; 34;1546-1558 (*:Equal contribution). 

Dan Yu, Gundeep Kaur, Robert M Blumenthal, Xing Zhang, and Xiaodong Cheng. Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. Journal of Biological Chemistry. 2021 (Manuscript accepted). 

Reproducible and Characterized Method for Ponatinib Encapsulation into Biomimetic Lipid Nanoparticles as a Platform for Multi-Tyrosine Kinase-Targeted Therapy. Assaf Zinger, Gherardo Baudo, Tomoyuki Naoi, Federica Giordano, Stefania Lenna, Matteo Massaro, April Ewing, Ha Ram Kim, Ennio Tasciotti, Jason T. Yustein, and Francesca Taraballi. ACS Applied Bio Materials 2020 3 (10), 6737-6745, DOI: 10.1021/acsabm.0c00685

Yu, X., Yi, P., Hamilton, R. A., Shen, H., Chen, M., Foulds, C. E., Mancini, M. A., Ludtke, S. J., Wang, Z., O’Malley, B. W. Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes. Mol. Cell (2020) 79, 812-823.

Pan Y, Ren Z, Gao S, Shen J, Wang L, Xu Z, Yu Y, Bachina P, Zhang H, Fan X, Laganowsky A, Yan N, Zhou M. Structural basis of ion transport and inhibition in ferroportin. Nat Commun. 2020 Nov 10;11(1):5686. doi: 10.1038/s41467-020-19458-6. PMID: 33173040; PMCID: PMC7655804.

Shen J, Wu G, Tsai AL, Zhou M. Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase. J Mol Biol. 2020 Aug 21;432(18):5152-5161. doi: 10.1016/j.jmb.2020.05.017. Epub 2020 May 27. PMID: 32470559; PMCID: PMC7483794.

Wang L, Qian H, Nian Y, Han Y, Ren Z, Zhang H, Hu L, Prasad BVV, Laganowsky A, Yan N, Zhou M. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature. 2020 May;581(7808):329-332. doi: 10.1038/s41586-020-2280-2. Epub 2020 May 13. PMID: 32433610; PMCID: PMC7255049.

Zhang H, Pan Y, Hu L, Hudson MA, Hofstetter KS, Xu Z, Rong M, Wang Z, Prasad BVV, Lockless SW, Chiu W, Zhou M. TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential. Nat Commun. 2020 Jan 28;11(1):547. doi: 10.1038/s41467-019-14240-9. PMID: 31992706; PMCID: PMC6987127.

Kumar, D., Yu, X., Crawford, S.E., Moreno, R. Jakana, J., Sankaran, B., Ramakrishnan, A., Kuandal., S., Estes, M.K., Zhao, W., and Prasad, B.V.V. (2019).  2.7 Å Cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity.  Science Advances, in press.

Hanzhi Z., Yaping P., Liya H., M. A. H., Katrina S. Hofstetter, Zhichun X., Mingqiang R., Zhao W., B. V. Venkataram P., Steve W. L., Wah C., & Ming Z. TrkA undergoes a tetramer-to-dimer conversion to open TrkH which might alter bacterial membrane potential. Nat Commun. in press 2019; 

Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. A complete data processing workflow for CryoET and subtomogram averaging. Nat. Method accepted. February 01, 2019. Available from: https://ui.adsabs.harvard.edu/\#abs/2019arXiv190203978C.

Xie Q, Wang Z, Ni F, Chen X, Ma J, Patel N, Lu H, Liu Y, Tian JH, Flyer D, Massare MJ, Ellingsworth L, Glenn G, Smith G, Wang Q. Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein. PLoS One. 2019;14(2):e0210749. Epub 2019/02/08. PubMed PMID: 30730999.

Meng R, Jiang M, Cui Z, Chang JY, Yang K, Jakana J, Yu X, Wang Z, Hu B, Zhang J. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat Commun. 2019;10(1):3130. Epub 2019/07/18. PubMed PMID: 31311931; PMCID: PMC6635492.

Dosey TL, Wang Z, Fan G, Zhang Z, Serysheva, II, Chiu W, Wensel TG. Structures of TRPV2 in distinct conformations provide insight into role of the pore turret. Nat Struct Mol Biol. 2019;26(1):40-9. Epub 2019/01/02. PubMed PMID: 30598551; PMCID: PMC6458597.

Robichaux MA, Potter VL, Zhang Z, He F, Liu J, Schmid MF, Wensel TG. Defining the layers of a sensory cilium with STORM and cryoelectron nanoscopy. Proc Natl Acad Sci U S A. 2019;116(47):23562-72. Epub 2019/11/07. PubMed PMID: 31690665; PMCID: PMC6876244.

Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC. Nat Commun. 2019;10(1):2635. Epub 2019/06/16. PubMed PMID: 31201302; PMCID: PMC6570770.

Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. J Cell Biol. 2018;217(8):2851-65. Epub 2018/06/15. PubMed PMID: 29899041; PMCID: PMC6080925.

Dosey TL, Wang Z, Fan G, Zhang Z, Serysheva II, Chiu W, Wensel TG. TRPV2 Ion Channel Gating Through Allosteric Domain Coupling Revealed by Cryo-EM. Available at SSRN 3155836. 2018.

Chen, M, Dai, W, Sun, SY, Jonasch, D, He, CY, Schmid, MF, Chiu, W, & Ludtke, SJ, Convolutional neural networks for automated annotation of cellular cryo-electron tomograms, Nature Methods, 2017

Jesus G. Galaz-Montoya, Steven J. Ludtke, The advent of structural biology in situ by single particle cryo-electron tomography, Biophys, 2017, Rep. doi:10.1007/s41048-017-0040-0

Wang, Z, Fan, G, Hryc, CF, Blaza, JN, Serysheva, II, Schmid, MF, Chiu, W, Luisi, BF, & Du, D, An allosteric transport mechanism for the AcrAB-1 TolC Multidrug Efflux Pump., ELife, 2017, PMCID5404916