Research Highlights

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4
Ubah, O. C., Lake, E. W., Gunaratne, G. S., Gallant, J. P., Fernie, M., Robertson, A. J., Marchant, J. S., Bold, T. D., Langlois, R. A., Matchett, W. E., Thiede, J. M., Shi, K., Yin, L., Moeller, N. H., Banerjee, S., Ferguson, L., Kovaleva, M., Porter, A. J., Aihara, H., LeBeau, A. M., and Barelle, C. J. (2021) Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography. Nat Commun. 12, 7325
Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2
Nabel, K. G., Clark, S. A., Shankar, S., Pan, J., Clark, L. E., Yang, P., Coscia, A., McKay, L. G. A., Varnum, H. H., Brusic, V., Tolan, N. V., Zhou, G., Desjardins, M., Turbett, S. E., Kanjilal, S., Sherman, A. C., Dighe, A., LaRocque, R. C., Ryan, E. T., Tylek, C., Cohen-Solal, J. F., Darcy, A. T., Tavella, D., Clabbers, A., Fan, Y., Griffiths, A., Correia, I. R., Seagal, J., Baden, L. R., Charles, R. C., and Abraham, J. (2021) Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science
7LIR
Li, T., Stayrook, S. E., Tsutsui, Y., Zhang, J., Wang, Y., Li, H., Proffitt, A., Krimmer, S. G., Ahmed, M., Belliveau, O., Walker, I. X., Mudumbi, K. C., Suzuki, Y., Lax, I., Alvarado, D., Lemmon, M. A., Schlessinger, J., and Klein, D. E. (2021) Structural basis for ligand reception by anaplastic lymphoma kinase. Nature. 600, 148-152
7N4I
Dussupt, V., Sankhala, R. S., Mendez-Rivera, L., Townsley, S. M., Schmidt, F., Wieczorek, L., Lal, K. G., Donofrio, G. C., Tran, U., Jackson, N. D., Zaky, W. I., Zemil, M., Tritsch, S. R., Chen, W. - H., Martinez, E. J., Ahmed, A., Choe, M., Chang, W. C., Hajduczki, A., Jian, N., Peterson, C. E., Rees, P. A., Rutkowska, M., Slike, B. M., Selverian, C. N., Swafford, I., Teng, I. - T., Thomas, P. V., Zhou, T., Smith, C. J., Currier, J. R., Kwong, P. D., Rolland, M., Davidson, E., Doranz, B. J., Mores, C. N., Hatziioannou, T., Reiley, W. W., Bieniasz, P. D., Paquin-Proulx, D., Gromowski, G. D., Polonis, V. R., Michael, N. L., Modjarrad, K., M Joyce, G., and Krebs, S. J. (2021) Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations. Nat Immunol. 10.1038/s41590-021-01068-z
7RQ8
Mitcheltree, M. J., Pisipati, A., Syroegin, E. A., Silvestre, K. J., Klepacki, D., Mason, J. D., Terwilliger, D. W., Testolin, G., Pote, A. R., J Y Wu, K., Ladley, R. Porter, Chatman, K., Mankin, A. S., Polikanov, Y. S., and Myers, A. G. (2021) A synthetic antibiotic class overcoming bacterial multidrug resistance. Nature. 10.1038/s41586-021-04045-6
7LFV
Patchett, S., Lv, Z., Rut, W., Békés, M., Drag, M., Olsen, S. K., and Huang, T. T. (2021) A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Cell Rep. 36, 109754
Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2
Ye, Q., Lu, S., and Corbett, K. D. (2021) Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol. 12, 719037
SARS-CoV-2 main protease in complex with N-terminal autoprocessing substrate
MacDonald, E. A., Frey, G., Namchuk, M. N., Harrison, S. C., Hinshaw, S. M., and Windsor, I. W. (2021) Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease. ACS Infect Dis. 10.1021/acsinfecdis.1c00237
Crystal structure of the SARS-CoV-2 (2019-NCoV) main protease in complex with 5-(3-{3-chloro-5-[(5-methyl-1,3-thiazol-4-yl)methoxy]phenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl)pyrimidine-2,4(1H,3H)-dione (compound 13)
Zhang, C. - H., Spasov, K. A., Reilly, R. A., Hollander, K., Stone, E. A., Ippolito, J. A., Liosi, M. - E., Deshmukh, M. G., Tirado-Rives, J., Zhang, S., Liang, Z., Miller, S. J., Isaacs, F., Lindenbach, B. D., Anderson, K. S., and Jorgensen, W. L. (2021) Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency. ACS Med Chem Lett. 12, 1325-1332
Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1
Ye, G., Gallant, J., Zheng, J., Massey, C., Shi, K., Tai, W., Odle, A., Vickers, M., Shang, J., Wan, Y., Du, L., Aihara, H., Perlman, S., LeBeau, A., and Li, F. (2021) The development of Nanosota-1 as anti-SARS-CoV-2 nanobody drug candidates. Elife. 10.7554/eLife.64815
SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot
Roman, C., Lewicka, A., Koirala, D., Li, N. - S., and Piccirilli, J. A. (2021) The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography.. ACS Chem Biol. 10.1021/acschembio.1c00324
CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 23
Deshmukh, M. G., Ippolito, J. A., Zhang, C. - H., Stone, E. A., Reilly, R. A., Miller, S. J., Jorgensen, W. L., and Anderson, K. S. (2021) Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease. Structure. 10.1016/j.str.2021.06.002
Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH)
Viswanathan, T., Misra, A., Chan, S. - H., Qi, S., Dai, N., Arya, S., Martinez-Sobrido, L., and Gupta, Y. K. (2021) A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide. Nat Commun. 12, 3287
Structure of human PARG complexed with PARG-292, 7KG7
Brosey, C. A., Houl, J. H., Katsonis, P., Balapiti-Modarage, L. P. F., Bommagani, S., Arvai, A., Moiani, D., Bacolla, A., Link, T., Warden, L. S., Lichtarge, O., Jones, D. E., Ahmed, Z., and Tainer, J. A. (2021) Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Prog Biophys Mol Biol. 10.1016/j.pbiomolbio.2021.02.002
CRYSTAL STRUCTURE OF THE SARS-COV-2(2019-NCOV) MAIN PROTEASE IN COMPLEX WITH COMPOUND 5
Zhang, C. - H., Stone, E. A., Deshmukh, M., Ippolito, J. A., Ghahremanpour, M. M., Tirado-Rives, J., Spasov, K. A., Zhang, S., Takeo, Y., Kudalkar, S. N., Liang, Z., Isaacs, F., Lindenbach, B., Miller, S. J., Anderson, K. S., and Jorgensen, W. L. (2021) Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS Cent Sci. 7, 467-475
Crystal structure of SARS-CoV-2 3CL protease in complex with MAC5576
Iketani, S., Forouhar, F., Liu, H., Hong, S. Jung, Lin, F. - Y., Nair, M. S., Zask, A., Huang, Y., Xing, L., Stockwell, B. R., Chavez, A., and Ho, D. D. (2021) Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Commun. 12, 2016
Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)
Cerutti, G., Guo, Y., Zhou, T., Gorman, J., Lee, M., Rapp, M., Reddem, E. R., Yu, J., Bahna, F., Bimela, J., Huang, Y., Katsamba, P. S., Liu, L., Nair, M. S., Rawi, R., Olia, A. S., Wang, P., Zhang, B., Chuang, G. - Y., Ho, D. D., Sheng, Z., Kwong, P. D., and Shapiro, L. (2021) Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe. 10.1016/j.chom.2021.03.005
Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
Rapp, M., Guo, Y., Reddem, E. R., Yu, J., Liu, L., Wang, P., Cerutti, G., Katsamba, P., Bimela, J. S., Bahna, F. A., Mannepalli, S. M., Zhang, B., Kwong, P. D., Huang, Y., Ho, D. D., Shapiro, L., and Sheng, Z. (2021) Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class. Cell Rep. 10.1016/j.celrep.2021.108950
Crystal structure of apo Card1
Rostøl, J. T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R., Patel, D. J., and Marraffini, L. A. (2021) The Card1 nuclease provides defence during type III CRISPR immunity.. Nature. 590, 624-629
7LTU
Tayeb-Fligelman, E., Cheng, X., Tai, C., Bowler, J. T., Griner, S., Sawaya, M. R., Seidler, P. M., Jiang, Y. Xiao, Lu, J., Rosenberg, G. M., Salwinski, L., Abskharon, R., Zee, C. - T., Hou, K., Li, Y., Boyer, D. R., Murray, K. A., Falcon, G., Anderson, D. H., Cascio, D., Saelices, L., Damoiseaux, R., Guo, F., and Eisenberg, D. S. (2021) Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2. bioRxiv. 10.1101/2021.03.05.434000
Human SAMHD1 bound to ribo(CGCCU)-oligonucleotide
Yu, C. H., Bhattacharya, A., Persaud, M., Taylor, A. B., Wang, Z., Bulnes-Ramos, A., Xu, J., Selyutina, A., Martinez-Lopez, A., Cano, K., Demeler, B., Kim, B., Hardies, S. C., Diaz-Griffero, F., and Ivanov, D. N. (2021) Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification. Nat Commun. 12, 731
6X9Z PDB Structure
Vorobieva, A. A., White, P., Liang, B., Horne, J. E., Bera, A. K., Chow, C. M., Gerben, S., Marx, S., Kang, A., Stiving, A. Q., Harvey, S. R., Marx, D. C., G Khan, N., Fleming, K. G., Wysocki, V. H., Brockwell, D. J., Tamm, L. K., Radford, S. E., and Baker, D. (2021) De novo design of transmembrane β barrels.. Science. 10.1126/science.abc8182
Nesprin-2G(aa1425-1649)-FHOD1(aa1-339) complex, H. sapiens
Lim, S. Mei, Cruz, V. E., Antoku, S., Gundersen, G. G., and Schwartz, T. U. (2021) Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins. Structure. 10.1016/j.str.2020.12.013
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab)
Clark, S. A., Clark, L. E., Pan, J., Coscia, A., McKay, L. G. A., Shankar, S., Johnson, R. I., Griffiths, A., and Abraham, J. (2021) SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms. Cell. 10.1101/2020.11.13.381533
6PNK Structure
Lin, L. Yingqi, McCarthy, S., Powell, B. M., Manurung, Y., Xiang, I. M., Dean, W. L., Chaires, B., and Yatsunyk, L. A. (2020) Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX. PLoS One. 15, e0241513
6WV3
Liu, S., Li, S., Shen, G., Sukumar, N., Krezel, A. M., and Li, W. (2020) Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Science. 10.1126/science.abc5667
6WX4
Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S. J., Oualid, F. El, Huang, T. T., Békés, M., Drag, M., and Olsen, S. K. (2020) Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design. Sci Adv. 10.1126/sciadv.abd4596
Crystal Structure of Human Protocadherin-15 EC2-
Choudhary, D., Narui, Y., Neel, B. L., Wimalasena, L. N., Klanseck, C. F., De-la-Torre, P., Chen, C., Araya-Secchi, R., Tamilselvan, E., and Sotomayor, M. (2020) Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception. Proc Natl Acad Sci U S A. 10.1073/pnas.1920444117
6W70
Polizzi, N. F., and DeGrado, W. F. (2020) A defined structural unit enables de novo design of small-molecule-binding proteins. Science. 369, 1227-1233
6WZQ
Ye, Q., West, A. M. V., Silletti, S., and Corbett, K. D. (2020) Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Protein Sci. 10.1002/pro.3909
M Joyce, G., Sankhala, R. S., Chen, W. - H., Choe, M., Bai, H., Hajduczki, A., Yan, L., Sterling, S. L., Peterson, C. E., Green, E. C., Smith, C., de Val, N., Amare, M., Scott, P., Laing, E. D., Broder, C. C., Rolland, M., Michael, N. L., and Modjarrad, K. (2020) A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein. bioRxiv. 10.1101/2020.03.15.992883
6WKS
Viswanathan, T., Arya, S., Chan, S. - H., Qi, S., Dai, N., Misra, A., Park, J. - G., Oladunni, F., Kovalskyy, D., Hromas, R. A., Martinez-Sobrido, L., and Gupta, Y. K. (2020) Structural basis of RNA cap modification by SARS-CoV-2. Nat Commun. 11, 3718
Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate
Kim, S. - A., Zhu, J., Yennawar, N., Eek, P., and Tan, S. (2020) Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate. Mol Cell. 10.1016/j.molcel.2020.04.019
Structure of 2019-nCoV chimeric receptor-binding domain complexed with its receptor human ACE2
Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., and Li, F. (2020) Structural basis of receptor recognition by SARS-CoV-2. Nature. 10.1038/s41586-020-2179-y
Crystal Structure of the Klebsiella pneumoniae LpxH-lipid X complex
Cho, J., Lee, M., C Cochrane, S., Webster, C. G., Fenton, B. A., Zhao, J., Hong, J., and Zhou, P. (2020) Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics. Proc Natl Acad Sci U S A. 117, 4109-4116

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