Publications

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

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PNCC Publications

2021

  1. 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.
  2. 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.
  3. 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.
  4. Hu, Q., Botuyan, M. V., Zhao, D., Cui, G., Mer, E., Mer, G. (2021). Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Nature.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Hu, W., Parkinson, C., Zheng, H. (2021) Mechanistic Insights Revealed by YbtPQ in the Occluded State. Preprint on bioRxiv.
  11. Hu, W., Zheng, H. (2021) Cryo-EM Structure of a Ferrichrome Importer FhuCDB. Preprint on bioRxiv.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. Sung. M. W., Yang, Z., 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. Preprint on bioRxiv.
  17. Yu J, Rao P, Clark S, Mitra J, Ha T, Gouaux E. (2021) Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Nature.
  18. Wiryanman, T. & Toor, N. (2021). Cryo-EM structure of a thermostable bacterial nanocompartment. IUCrJ.
  19. Yang, C., Fyjiwara, R., Kim, H. J., Gorbea Colon, J. J., Steimle, S., Garcia, B. A., Murakami, K. (2021). Structural visualization of de novo initiation of RNA polymerase II transcription. Preprint on bioRxiv.
  20. 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.
  21. 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.
  22. 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.
  23. Abdella, R., Talyzina, A., Chen, S., Inouye, C. J., Tjian, R., & He, Y. (2021). Structural of the human Mediator-bound transcription preinitiation complex. Science.
  24. 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.
  25. 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.
  26. 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.
  27. Sharif, H., Hollingsworth, L. R., Griswold, A. R., Hsiao, J. C., Wang, Q., Bachovchin, D. A., & Wu, H. (2021). Structural mechanism of CARD8 regulation by DPP9. Preprint on bioRxiv.
  28. 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.
  29. Sweet, M. E., Larsen, C., Zhang, X., Schlame, M., Pedersen, B. P., & Stokes, D. L. (2021). Structural basis for Potassium transport by KdpFABC. Preprint on bioRxiv.
  30. 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. Bonilla, S., Sherlock, M. E., MacFadden, A., & Kieft, J. S. (2020). A structured viral RNA uses molecular mimicry and conformational dynamics to coordinate multiple functions. Preprint on bioRxiv.
  3. 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.
  4. 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.
  5. Eygeris, Y., Patel, S., Jozic, A., & Sahay, G. (2020). Deconvoluting Lipid Nanoparticle Structure for Messenger RNA Delivery. ACS Publications.
  6. 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.
  7. Herrera, M., Kim, J., Eygeris, Y., Jozic, A., & Sahay, G. (2020). Illuminating endosomal escape of polymorphic lipid nanoparticles that boost mRNA delivery. Biomaterials Science.
  8. 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. (2020). DPP9 directly sequesters the NLRP1 C-terminus to repress inflammasome activation. Preprint on bioRxiv.
  9. 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.
  10. Kato, K., Ahmad, S., Zhu, Z., Young, J. M., Mu, X., Park, S., Malik, H. S., & Hur, S. (2020). Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Molecular Cell.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. Sobti, M., Walshe, J. L., Zeng, Y. C., Ishmukhametov, R., & Stewart, A. G. (2020). Subunit epsilon of E. coli F1Fo ATP synthase attenuates enzyme activity by modulating central stalk flexibility. Preprint on bioRxiv.
  19. 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.
  20. Wang, C., Molodtsov, V., Firlar, E., Kaelber, J., Blaha, G., Su, M., & Ebright, R. H. (2020). Structural basis of transcription-translation coupling. Science.
  21. Yang, X., Wang, Q., & Cao, E. (2020). Structure of the human cation-chloride cotransporter NKCC1 determined by single-particle electron cryo-microscopy. Nature Communications.
  22. 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. bioRxiv, 2020.08.06.240481. Preprint on bioRxiv.
  23. 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.
  24. 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.