xia2: an expert system for macromolecular crystallography data reduction

Overview of the CCP 4 suite and current developments

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

Barnes, C. O., Jette, C. A., Abernathy, M. E., Dam, K.-M. A., Esswein, S. R., Gristick, H. B., Malyutin, A. G., Sharaf, N. G., Huey-Tubman, K. E., Lee, Y. E., et al. (2020) · Nature · doi:10.1038/s41586-020-2852-1 · Cited by 1,599

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Dejnirattisai, W., Huo, J., Zhou, D., Zahradník, J., Supasa, P., Liu, C., Duyvesteyn, H. M. E., Ginn, H. M., Mentzer, A. J., Tuekprakhon, A., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.046 · Cited by 930

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Liu, C., Ginn, H. M., Dejnirattisai, W., Supasa, P., Wang, B., Tuekprakhon, A., Nutalai, R., Zhou, D., Mentzer, A. J., Zhao, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.020 · Cited by 669

Antibody evasion by the P.1 strain of SARS-CoV-2

Dejnirattisai, W., Zhou, D., Supasa, P., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Tuekprakhon, A., Nutalai, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.055 · Cited by 583

Molecular basis of USP7 inhibition by selective small-molecule inhibitors.

Turnbull, A. P., Ioannidis, S., Krajewski, W. W., Pinto-Fernandez, A., Heride, C., Martin, A. C. L., Tonkin, L. M., Townsend, E. C., Buker, S. M., Lancia, D. R., et al. (2017) · Nature · doi:10.1038/nature24451 · Cited by 463

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

Supasa, P., Zhou, D., Dejnirattisai, W., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Nutalai, R., Tuekprakhon, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.033 · Cited by 460

The antigenic anatomy of SARS-CoV-2 receptor binding domain

Dejnirattisai, W., Zhou, D., Ginn, H. M., Duyvesteyn, H. M. E., Supasa, P., Case, J. B., Zhao, Y., Walter, T. S., Mentzer, A. J., Liu, C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.032 · Cited by 371

De novo design of a fluorescence-activating β-barrel

Dou, J., Vorobieva, A. A., Sheffler, W., Doyle, L. A., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Gagnon, L. A., et al. (2018) · Nature · doi:10.1038/s41586-018-0509-0 · Cited by 351

Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

Zhou, D., Duyvesteyn, H. M. E., Chen, C.-P., Huang, C.-G., Chen, T.-H., Shih, S.-R., Lin, Y.-C., Cheng, C.-Y., Cheng, S.-H., Huang, Y.-C., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0480-y · Cited by 274

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

Bussiere, D. E., Xie, L., Srinivas, H., Shu, W., Burke, A., Be, C., Zhao, J., Godbole, A., King, D., Karki, R. G., et al. (2020) · Nature Chemical Biology · doi:10.1038/s41589-019-0411-6 · Cited by 257

Structure-guided development of a potent and selective non-covalent active-site inhibitor of USP7.

Lamberto, I., Liu, X., Seo, H.-S., Schauer, N. J., Iacob, R. E., Hu, W., Das, D., Mikhailova, T., Weisberg, E. L., Engen, J. R., et al. (2017) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.09.003 · Cited by 192

The Molecular Basis for the Endocytosis of Small R-SNAREs by the Clathrin Adaptor CALM

Miller, S. E., Sahlender, D. A., Graham, S. C., Höning, S., Robinson, M. S., Peden, A. A., & Owen, D. J. (2011) · Cell · doi:10.1016/j.cell.2011.10.038 · Cited by 192

PCNA directs type 2 RNase H activity on DNA replication and repair substrates

Bubeck, D., Reijns, M. A. M., Graham, S. C., Astell, K. R., Jones, E. Y., & Jackson, A. P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq980 · Cited by 144

A covalent inhibitor of K-Ras(G12C) induces MHC class I presentation of haptenated peptide neoepitopes targetable by immunotherapy

Zhang, Z., Rohweder, P. J., Ongpipattanakul, C., Basu, K., Bohn, M.-F., Dugan, E. J., Steri, V., Hann, B., Shokat, K. M., & Craik, C. S. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.07.005 · Cited by 136

Structural basis for kinesin-1:cargo recognition

Pernigo, S., Lamprecht, A., Steiner, R. A., & Dodding, M. P. (2013) · Science · doi:10.1126/science.1234264 · Cited by 117

Computational design of epitope-specific functional antibodies

Nimrod, G., Fischman, S., Austin, M., Herman, A., Keyes, F., Leiderman, O., Hargreaves, D., Strajbl, M., Breed, J., Klompus, S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.10.081 · Cited by 77

Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity

Vognsen, T., Møller, I. R., & Kristensen, O. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080947 · Cited by 73

A YidC-like protein in the archaeal plasma membrane.

Borowska, M. T., Dominik, P. K., Anghel, S. A., Kossiakoff, A. A., & Keenan, R. J. (2015) · Structure · doi:10.1016/j.str.2015.06.025 · Cited by 71

Aster-dependent nonvesicular transport facilitates dietary cholesterol uptake

Ferrari, A., Whang, E., Xiao, X., Kennelly, J. P., Romartinez-Alonso, B., Mack, J. J., Weston, T., Chen, K., Kim, Y., Tol, M. J., et al. (2023) · Science · doi:10.1126/science.adf0966 · Cited by 61

The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs

Lingaraju, M., Johnsen, D., Schlundt, A., Langer, L. M., Basquin, J., Sattler, M., Heick Jensen, T., Falk, S., & Conti, E. (2019) · Nature Communications · doi:10.1038/s41467-019-11339-x · Cited by 55

Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases

Hespanhol, J. T., Sanchez-Limache, D. E., Nicastro, G. G., Mead, L., Llontop, E. E., Chagas-Santos, G., Farah, C. S., de Souza, R. F., Galhardo, R. D. S., Lovering, A. L., et al. (2022) · eLife · doi:10.7554/elife.82437 · Cited by 45

A CLC-type F-/H+ antiporter in ion-swapped conformations

Last, N. B., Stockbridge, R. B., Wilson, A. E., Shane, T., Kolmakova-Partensky, L., Koide, A., Koide, S., & Miller, C. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0082-0 · Cited by 45

Selective Aster inhibitors distinguish vesicular and nonvesicular sterol transport mechanisms

Xiao, X., Kim, Y., Romartinez-Alonso, B., Sirvydis, K., Ory, D. S., Schwabe, J. W. R., Jung, M. E., & Tontonoz, P. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024149118 · Cited by 40

Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation

(2023) · doi:10.1073/pnas.2310664120 · Cited by 27

Molecular determinants of permeation in a fluoride-specific ion channel

Last, N. B., Sun, S., Pham, M. C., & Miller, C. (2017) · eLife · doi:10.7554/elife.31259 · Cited by 25

Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism

Dolan, S. K., Wijaya, A., Kohlstedt, M., Gläser, L., Brear, P., Silva-Rocha, R., Wittmann, C., & Welch, M. (2022) · mBio · doi:10.1128/mbio.02541-22 · Cited by 21

Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence

(2024) · doi:10.1038/s41467-024-51629-7 · Cited by 18

A communication hub for phosphoregulation of kinetochore-microtubule attachment

(2024) · doi:10.1016/j.cub.2024.04.067 · Cited by 17

Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes

Silale, A., Zhu, Y., Witwinowski, J., Smith, R. E., Newman, K. E., Bhamidimarri, S. P., Baslé, A., Khalid, S., Beloin, C., Gribaldo, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42601-y · Cited by 16

Structural and regulatory insights into the glideosome-associated connector from Toxoplasma gondii

Kumar, A., Vadas, O., Dos Santos Pacheco, N., Zhang, X., Chao, K., Darvill, N., Rasmussen, H. Ø., Xu, Y., Lin, G. M.-H., Stylianou, F. A., et al. (2023) · eLife · doi:10.7554/elife.86049 · Cited by 15

Elucidating polymorphs of crystal structures by intensity-based hierarchical clustering analysis of multiple diffraction data sets

Matsuura, H., Sakai, N., Toma-Fukai, S., Muraki, N., Hayama, K., Kamikubo, H., Aono, S., Kawano, Y., Yamamoto, M., & Hirata, K. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323007039 · Cited by 14

Nicotine biosynthesis is completed by cryptic activating glucosylation

Schwabe, B. T. W., Angstman, I. M., Vollheyde, K., Ingold, Z., Li, J., Stankevich, K. S., Spicer, C. D., Fascione, M. A., Grogan, G., Geu-Flores, F., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72705-0 · Cited by 12

Designing novel solenoid proteins with in silico evolution

(2025) · doi:10.1038/s42004-025-01817-3 · Cited by 10

The structure of an amyloid precursor protein/talin complex indicates a mechanical basis of Alzheimer’s disease

(2024) · doi:10.1098/rsob.240185 · Cited by 9

Structural similarities between the metacyclic and bloodstream form variant surface glycoproteins of the African trypanosome

Chandra, M., Đaković, S., Foti, K., Zeelen, J. P., van Straaten, M., Aresta-Branco, F., Tihon, E., Lübbehusen, N., Ruppert, T., Glover, L., et al. (2023) · PLOS Neglected Tropical Diseases · doi:10.1371/journal.pntd.0011093 · Cited by 8

The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds

(2022) · doi:10.1099/jgv.0.001716 · Cited by 8

Engineering of soluble bacteriorhodopsin

Nikolaev, A., Orlov, Y., Tsybrov, F., Kuznetsova, E., Shishkin, P., Kuzmin, A., Mikhailov, A., Nikolaeva, Y. S., Anuchina, A., Chizhov, I., et al. (2025) · Chemical Science · doi:10.1039/d5sc02453f · Cited by 6

Divergent polo boxes in KKT2 bind KKT1 to initiate the kinetochore assembly cascade in Trypanosoma brucei

Ishii, M., Ludzia, P., Marcianò, G., Allen, W., Nerusheva, O. O., & Akiyoshi, B. (2022) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-07-0269-t · Cited by 5

Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like β-lactamases

Hoff, J. F., Goudar, K. E., Calvopiña, K., Beer, M., Hinchliffe, P., Shaw, J. M., Tooke, C. L., Takebayashi, Y., Cadzow, A. F., Harmer, N. J., et al. (2025) · RSC Medicinal Chemistry · doi:10.1039/d5md00512d · Cited by 3

Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis

Rahman, M. A., Dalwani, S., & Venkatesan, R. (2025) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2025.151960 · Cited by 3

A small molecule PTER-selective inhibitor reduces food intake and body weight

Fu, S., Wang, L., Li, V. L., Lyu, X., Wei, W., Shi, X., Deng, S., Barber, J. L., Tahir, U. A., Adams, C., et al. (2026) · Cell Chemical Biology · doi:10.1016/j.chembiol.2026.02.005 · Cited by 2

A small molecule PTER-selective inhibitor reduces food intake and body weight

Fu, S., Wang, L., Li, V. L., Lyu, X., Wei, W., Shi, X., Deng, S., Barber, J. L., Tahir, U. A., Adams, C., et al. (2026) · doi:10.64898/2026.01.26.701829 · Cited by 2

A viral SAVED protein with ring nuclease activity degrades the CRISPR second messenger cA4

(2025) · doi:10.1042/bcj20253271 · Cited by 1

Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii

Stuart, W. S., Jenkins, C. H., Ireland, P. M., Isupov, M. N., Norville, I. H., & Harmer, N. J. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108517 · Cited by 1