Publications listed represent all or part of the research that was carried out using PNCC resources.

Check out PNCC Usage Disclaimers for information regarding acknowledgements, data sharing & publications.

 


PNCC Publications

2022

  1. Kwon, D. H., Zhang, F., Fedor, J. G., Suo, Y., Lee, S.Y. (2022). Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis. Nature.
  2. Zhao, Y., Roy, K., Vidossich, P., Cancedda, L., De Vivo, M., Forbush, B., Cao, E. (2022). Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide. Nature.
  3. Xu, Y., Han, H., Cooney, I., Guo, Y., Moran, N. G., Zuniga, N. R., Price, J. C., Hill, C. P., Shen, P. S. (2022). Active conformation of the p97-p47 unfoldase complex. Nature.
  4. Jeong, H., Clark, S., Goehring, A., Dehghani-Ghahnaviyeh, S., Rasouli, A., Tajkhorshid, E., Gouaux, E. (2022). Structure of C. elegans TMC-I complex illuminates auditory mechanosensory transduction. Preprint on bioRxiv.
  5. Mahfurzur Rahman, M. D., Basta, T., Teng, J., Lee, M., Worrell, B. T., Stowell, M. H. B., Hibbs, R. E. (2022). Structural mechanism of muscle nicotinic receptor desensitization and block by curare. Nature.
  6. Courbet, A., Hansen, J., Hsia, Y., Bethel, N., Park, Y.-J., Xu, C., Moyer, A., Boyken, S. E., Ueda, G., Nattermann, U., Nagarajan, D., Silva, D.-A., Sheffler, W., Quispe, J., Nord, A., King, N., Bradley, P., Vessler, D., Kollman, J., Baker, D. (2022). Computational design of mechanically coupled axle-rotor protein assemblies. Science.
  7. Ruben, E. A., Summers, B., Rau, M. J., Fitzpatrick, J. A. J., Di Cera, E. (2022). Cryo-EM structure of the prothrombin-prothrombinase complex. Blood.
  8. Brawley, D. N., Sauer, D. B., Lu, J., Zheng, X., Koide, A., Jedhe, G. S., Suwatthee, T., Song, J., Arora, P. S., Koide, S., Torres, V. J., Wang, D-N., Traaseth, N., J. (2022). Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus. Nature.
  9. Koo, C. W., Tucci, F. J., He, Y., Rosenzweig, A. C. (2022). Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science.
  10. Rahman, M. M., Basta, T., Teng, J., Lee, M., Worrell, B. T., Stowell, M. H. B., Hibbs, R. E. (2022). Structural mechanism of muscle nicotinic receptor desensitization and block by curare. Nature.
  11. Khandelwal, N. K., Millan, C. R., Zangari, S. I., Avila, S., Williams, D., Thaker, T. M., Tomasiak, T. M. (2022). The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation. Nature.
  12. Weaver, T. M., Hoitsmam N. M., Spencer, J. J., Gakhar, L., Schnicker, N. J., Freudenthal, B. D. (2022). Structural basis for APE1 processing DNA damage in the nucleosome. Preprint on bioRxiv.
  13. Ahn, E., Tang, T., Kim, B., Lee, H. J., Cho, U.-S. (2022). Development of an atmospheric plasma jet device for versatile treatment of electron microscope sample grids. JBC.
  14. Cruz, V. E., Sekulski, K., Peddada, N., Sailer, C., Balasubramanian, S., Weirich, C. S., Stengel, F., Erzberger, J. P. (2022). Sequence-directed RNA remodeling within a topologically complex RNP substrate. Preprint on bioRxiv.
  15. Gan, N., Han, Y., Zeng, W., Wang, Y., Xue, J., Jiang, Y. (2022). Structural mechanism of allosteric activation of TRPML1 by PI(3,5)P2 and rapamycin. PNAS.
  16. Wang, C., Polovitskaya, M. M., Delgado, B. D., Jentsch, T. J., Long, S. B. (2022). Gating choreography and mechanism of the human proton - activated chloride channel ASOR. Science.
  17. Morgan, C. E., Zhang, Z., Bonomo, R. A., Yu, E. W. (2022). An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii. ASM Journals.
  18. Yang, C., Fyjiwara, R., Kim, H. J., Basnet, P., Zhu, Y., Gorbea Colon, J. J., Steimle, S., Garcia, B. A., Kaplan, C. D., Murakami, K. (2022). Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Molecular Cell.
  19. Zane, G. M., Silveria, M. A., Meyer, N., White, T. A., Chapman, M. (2021). Cryo-EM Structure of Adeno-associated virus-4 at 2.2Å resolutionPreprint on bioRxiv.

2021

  1. Elferich, J., Clark, S., Ge, J., Goehring, A., Matsui, A., Gouaux, E. (2021). Molecular Structures and conformations of protocadherin-15 and its complexes on stereocilia elucidated by cryo-electron tomography. eLIFE.
  2. Thaker. T. M., Mishra, S., Zhou, W., Mohan, M., Tang, Q., Faraldo-Gomez, J. D., Mchaourab, H. S., Tomasiak, T. M. (2021). Asymmetric drug binding in an ATP-loaded inward-facing state of an ABC transporter. Nature.
  3. Hu, W., Zheng, H. (2021). Cryo-EM reveals unique structural features of the FhuCDB Escherichia coli ferrichrome importer. Nature.
  4. Yang, D., Gouaux, E. (2021). Illuminations of serotonin transporter mechanism and role of the allosteric site. Science Advances.
  5. Bonilla, S.L., Sherlock, M. E., MacFadden, A., & Kieft, J. S. (2021). A viral RNA hijacks host machinery using dynamic conformational changes of a t-RNA-like structure. Science.
  6. Sung, M. W., Yang, Z., Driggers, C. M., Patton, B. L., Mostofian, B., Russo, J., Zuckerman, D. M., Shyng, S-L. (2021) Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. PNAS.
  7. Neuberger, A., Nadezhdin, K. D., & Sobolevsky, A. I. (2021). Structural mechanisms of TRPV6 inhibition by ruthenium red and econazole. Nature Communications.
  8. Lewis, T.S., Sokolova, V., Jung, H., Ng, H., Tan, D. (2021). Structural basis of chromatin regulation by histone variant H2A.Z. Nucleic Acids Research.
  9. Scortecci, J.F., Molday, L.L., Curtis, S.B., Garces, F.A., Panwar, P., Petegem, F.V., Molday, R.S. (2021). Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nature Communications.
  10. Caffrey, B., Zhu, X., Berezuk, A., Tuttle, K., Chittori, S., Subramaniam, S. (2021). Common mutations of AAA ATPase p97 and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. Journal of Biological Chemistry.
  11. Plenge, P., Yang, D., Salomon, K., Laursen, L., Kalenderoglou, I. E., Newman, A. H., Gouaux, E., Coleman, J. A., Loland, C. J. (2021). The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. Nature.
  12. Su, C.-C., Klenotic, P. A., Cui, M., Lyu, M., Morgan C. E., Yu, E. W. (2021). Structures of the mycobacterial membrane protein MmpL3 reveal its mechanism of lipid transport. PLOS Biology.
  13. Hu, Q., Botuyan, M. V., Zhao, D., Cui, G., Mer, E., Mer, G. (2021). Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Nature.
  14. Sweet, M. E., Larsen, C., Zhang, X., Schlame, M., Pedersen, B. P., & Stokes, D. L. (2021). Structural basis for potassium transport in prokaryotes by KdpFABC. PNAS.
  15. Lopez-Redondo, M., Fan, S., Koide, A., Koide, S., Beckstein, O., & Stokes, D. L. (2020). Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. Journal of General Physiology.
  16. Sharif, H., Hollingsworth, L. R., Griswold, A. R., Hsiao, J. C., Wang, Q., Bachovchin, D. A., Wu, H. (2021). Dipeptidyl peptidase 9 sets a threshold for CARD8 inflammasome formation by sequestering its active C-terminal fragment. Immunity.
  17. Nadezhdin, K. D., Neuberger, A., Trofimov, Y. A., Krylov, N. A., Sinica, V., Kupko, N., Vlachova, V., Zakharian, E., Efremov, R. A., & Sobolevsky, A. I. (2021). Structural mechanisms of heat-induced opening of a temperature-sensitive TRP channel. Nature
  18. Kwon, D.H., Zhang, F., Suo, Y., Bouvette, J., Borgina, M. J., and Lee, S-Y. (2021) Heat-dependent opening of TRPV1 in the presence of capsaicin. Nature Structural & Molecular Biology.
  19. Khandelwal, N. K., Millan, C. R., Zangari, S. A., Williams, D., Thaker, T. M., Tomasiak, T. M. (2021) The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation. Preprint on bioRxiv.
  20. Chen, P., Zeng, J., Liu, Z., Thaker, H., Wang, S., Tian, S., Zhang, J., Tao, L., Gutierrez, C. B., Xing, L., Gerhard, R., Huang, L., Dong, M., and Jin, R. (2021) Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection. Nature Communications.
  21. Hu, W., Parkinson, C., Zheng, H. (2021) Mechanistic Insights Revealed by YbtPQ in the Occluded State. Preprint on bioRxiv.
  22. Hu, W., Zheng, H. (2021) Cryo-EM Structure of a Ferrichrome Importer FhuCDB. Preprint on bioRxiv.
  23. Faylo, J.L., van Eeuwen, T., Kim, H.J., Gorbea Colón, J.J., Garcia, B.A., Murakami, K., Christianson, D.W. (2021) Structural Insight on Assembly-Line Catalysis in Terpene Biosynthesis. Nature Communications.
  24. Shen, B. W., Quispe, J. D., Luyten, Y., McGough, B. E., Morgan, R. D., & Stoddard, B. L. (2021). Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM. Structure.
  25. Rathinaswamy, M. K., Dalwadi, U., Fleming, K. D., Adams, C., Stariha, J. TB., Pardon, E., Baek, M., Vadas, O., DiMaio, F., Steyaert, J., Hansen, S. D., Yip, C. K., Burke. J. E. (2021) Structure of the phosphoinositide 3-kinase p110γ-p101 complex reveals molecular mechanism of GPCR activation. Preprint on bioRxiv.
  26. Rathinaswamy, M. K., Fleming, K. D., Dalwadi, U., Pardon, E., Harris, N. J., Yip, C. K., Steyaert, J., Burke. J. E. (2021) HDX-MS optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases. Preprint on bioRxiv.
  27. Neuberger, A., Nadezhdin, K. D., & Sobolevsky, A. I. (2021). TRPV3 expression and purification for structure determination by Cryo-EM. Ion Channels: Channel Biochemistry, Reconstruction, and Function, 31.
  28. Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E. (2021) Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Nature.
  29. Wiryanman, T. & Toor, N. (2021). Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ.
  30. Noviello, C. M., Gharpure, A., Mukhtasimova, N., Cubuco, R., Baxter, L., Borek, D., Sine, S. M., & Hibbs, R. E. (2021). Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell.
  31. Chen, S., Lee, L., Naila, T., Fishbain, S., Wang, A., Tomkinson, A. E., Lees-Miller, S. P., & He, Y. (2021). Structural basis of long-range to stort-range synaptic transition in NHEJ. Nature.
  32. Osinski, A., Black, M. H., Pawłowski, K., Chen, Z., Li, Y., & Tagliabracci, V. S. (2021). Structural and mechanistic basis for protein glutamylation by the kinase fold. Preprint on bioRxiv.
  33. Abdella, R., Talyzina, A., Chen, S., Inouye, C. J., Tjian, R., & He, Y. (2021). Structural of the human Mediator-bound transcription preinitiation complex. Science.
  34. Liu, C., Reese, R., Vu, S., Rouge, L., Shields, S. D., Kakiuchi-Kiyota, S., Chen, H., Johnson, K., Shi, Y. P., Chernov-Rogan, T., Greiner, D. M. Z., Kohli, P. B., Hackos, D., Brillantes, B., Tam, C., Li, T., Wang, J., Safina, B., Magnuson, S., Volgraf, M., Payandeh, J., Zheng, J., Rohou, A., & Chen, J. (2021). A Non-covalent Ligand Reverals Biased Agonism of the TRPA1 Ion Channel. Neuron.
  35. Hollingsworth, L. R., David, L., Li, Y., Griswold, A. R., Sharif, H., Fontana, P., Fu, T., Ruan, J., Bachovchin, D. A., & Wu, H. (2021). Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 Inflammasomes. Nature Communications.
  36. Hollingsworth, L. R., Sharif, H., Griswold, A. R., Fontana, P., Mintseris, J., Dagbay, K. B., Paulo, J. A., Gygi, S. P., Bachovchin, D. A., & Wu, H. (2021). DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation. Nature.
  37. Sauer, D. B., Song, J., Wang, B., Hilton, J. K., Karpowich, N. K, Mindell, J. A., Rice, W. J., & Wang, D-N.(2021). Structure and inhibition mechanism of the human citrate transporter NaCT. Nature.
  38. Kato, K., Ahmad, S., Zhu, Z., Young, J. M., Mu, X., Park, S., Malik, H. S., & Hur, S. (2021). Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Molecular Cell.
  39. Herrera, M., Kim, J., Eygeris, Y., Jozic, A., & Sahay, G. (2021). Illuminating endosomal escape of polymorphic lipid nanoparticles that boost mRNA delivery. Biomaterials Science.
  40. Grau, D., Zhang, Y., Lee, C-H., Valencia-Sanchez, M., Zhang, J., Wang, M., Holder, M., Svetlov, V., Tan, D., Nudler, E., Reinberg, D., Walz, T., Armache, K-J. (2021). Structures of the monomeric and dimeric PRC2:EZH2 reveal flexible modules involved in chromatin compaction. Nature Communications.
  41. Travis, B. A., Ramsey, K. M.,Prezioso, S. M., Tallo, T., Wandzilak, J. M., Hsu, A., Borgnia, M., Bartesaghi, A., Dove, S. L., Brennan, R. G., & Schumacher, M. A. (2021). Structural Basis for Virulence Activation of Francisella tularensis. Molecular Cell.

 

2020

  1. Yoder, N., Jalali-Yazdi, F., Noreng, S., Houser, A., Baconguis, I., & Gouaux, E. (2020). Light-coupled cryo-plunger for time-resolved cryo-EM. Journal of Structural Biology.
  2. Coleman, J. A., Navratna, V., Antermite, D., Yang, D., Bull, J. A., & Gouaux, E. (2020). Chemical and structural investigation of the paroxetine-human serotonin transporter complex. eLife.
  3. Coudray, N., Isom, G. L., MacRae, M. R., Saiduddin, M. N., Bhabha, G., & Ekiert, D. C. (2020). Structure of bacterial phospholipid transporter MlaFEDB with substrate bound. Preprint on bioRxiv.
  4. Eygeris, Y., Patel, S., Jozic, A., & Sahay, G. (2020). Deconvoluting Lipid Nanoparticle Structure for Messenger RNA Delivery. ACS Publications.
  5. Flores, J. A., Haddad, B. G., Dolan, K. A., Myers, J. B., Yoshioka, C. C., Copperman, J., Zuckerman, D. M., & Reichow, S. L. (2020). Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å. Nature Communications.
  6. Jette, C. A., Barnes, C. O., Kirk, S. M., Melillo, B., Smith, A. B., & Bjorkman, P. J. (2020). Cryo-EM Structures of HIV-1 trimer bound to CD4-mimetics M48U1 and BNM-III-170 adopt a CD4-bound open conformation. Preprint on bioRxiv.
  7. Kim, J. J., Gharpure, A., Teng, J., Zhuang, Y., Howard, R. J., Zhu, S., Noviello, C., Walsh Jr, R. M., Lindahl, E., & Hibbs, R. E. (2020). Shared structural mechanisms of general anaesthetics and benzodiazepines. Nature.
  8. Novikova, I. V., Zhou, M., Du, C., Parra, M., Kim, D. N., VanAernum, Z. L., Shaw, J. B., Hellmann, H., Wysocki, V. H., & Evans, J. E. (2020). Tunable hetero-assembly of a plant pseudoenzyme-enzyme complex. Preprint on bioRxiv.
  9. Rahman, M. M., Teng, J., Worrell, B. T., Noviello, C. M., Lee, M., Karlin, A., Stowell, M. H. B., & Hibbs, R. E. (2020). Structure of the Native Muscle-type Nicotinic Receptor and Inhibition by Snake Venom Toxins. Neuron.
  10. Santosh, V., Musayev, F., Jaiswal, R., Zárate-Pérez, F., Vandewinkel, B., Dierckx, C., Endicott, M., Sharifi, K., Dryden, K., Henckaerts, E., & Escalante, C. R. (2020). The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states. Nucleic Acids Research.
  11. Silveria, M. A., Large, E. E., Zane, G. M., White, T. A., & Chapman, M. S. (2020). The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors. Viruses.
  12. Wang, Z., Rahkola, J., Redzic, J. S., Chi, Y-C., Tran, N., Holyoak, T., & Zheng, H. (2020). Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease. Nature Communications.
  13. Sobti, M., Walshe, J. L., Ishmukhametov, R., & Stewart, A. G. (2020). Visualizing movements in E. coli F1Fo ATP synthase indicates how the F1 and Fo motors are coupled. Nature Communications.
  14. Unchwaniwala, N., Zhan, H., Pennington, J., Horswill, M., den Boon, J. A., & Ahlquist, P. (2020). Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication. PNAS.
  15. Wang, C., Molodtsov, V., Firlar, E., Kaelber, J., Blaha, G., Su, M., & Ebright, R. H. (2020). Structural basis of transcription-translation coupling. Science.
  16. Yang, X., Wang, Q., & Cao, E. (2020). Structure of the human cation-chloride cotransporter NKCC1 determined by single-particle electron cryo-microscopy. Nature Communications.
  17. Yang, J. E., Larson, M. R., Sibert, B. S., Shrum, S., & Wright, E. R. (2020). CorRelator: An interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy. Preprint on bioRxiv.
  18. Yoder, N., & Gouaux, E. (2020). Conserved His-Gly motif of acid-sensing ion channels resides in a reentrant ‘loop’ implicated in gating and ion selectivity. eLife.
  19. Zhao, Y., Shen, J., Wang, Q., Zhou, M., & Cao, E. (2020). Inhibitory and Transport Mechanisms of the Human Cation-Chloride Cotransport KCC1. Preprint on bioRxiv.

 

2019

  1. Novikova, I., Zhou, M., Shaw, J., Hellmann, H., & Evans, J. E. (2019). Dual Native MS and Cryo-EM Approach to Resolve Heteromeric Protein Assemblies and Subunit Stoichiometry. Cambridge University Press.
  2. Patel, A. B., Moore, C. M., Greber, B. J., Luo, J., Ranish, J., & Nogales, E. (2019). Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. eLife.
  3. Yoshioka, C. (2019). Introducing the Pacific Northwest Center for Cryo-EM. Cambridge University Press.