ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

Coot : model-building tools for molecular graphics

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PHENIX : a comprehensive Python-based system for macromolecular structure solution

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MolProbity : all-atom structure validation for macromolecular crystallography

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Overview of the CCP 4 suite and current developments

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Towards automated crystallographic structure refinement with phenix.refine

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

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Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

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Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

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Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

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Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike

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N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

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A structural biology community assessment of AlphaFold2 applications

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Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686

Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

Wang, P., Casner, R. G., Nair, M. S., Wang, M., Yu, J., Cerutti, G., Liu, L., Kwong, P. D., Huang, Y., Shapiro, L., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.04.007 · Cited by 636

Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies

Wrapp, D., De Vlieger, D., Corbett, K. S., Torres, G. M., Wang, N., Van Breedam, W., Roose, K., van Schie, L., Hoffmann, M., Pöhlmann, S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.031 · Cited by 610

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., et al. (2022) · Science · doi:10.1126/science.abn8652 · Cited by 535

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A. C., Di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · Science · doi:10.1126/science.abi7994 · Cited by 412

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., Buczak, K., Schmidt, F. H., Margiotta, E., Mackmull, M.-T., et al. (2022) · Science · doi:10.1126/science.abm9506 · Cited by 355

Targeted protein degradation via intramolecular bivalent glues

Hsia, O., Hinterndorfer, M., Cowan, A. D., Iso, K., Ishida, T., Sundaramoorthy, R., Nakasone, M. A., Imrichova, H., Schätz, C., Rukavina, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07089-6 · Cited by 222

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline

Guo, H., Courbon, G. M., Bueler, S. A., Mai, J., Liu, J., & Rubinstein, J. L. (2021) · Nature · doi:10.1038/s41586-020-3004-3 · Cited by 200

Seeded assembly in vitro does not replicate the structures of α‐synuclein filaments from multiple system atrophy

Lövestam, S., Schweighauser, M., Matsubara, T., Murayama, S., Tomita, T., Ando, T., Hasegawa, K., Yoshida, M., Tarutani, A., Hasegawa, M., et al. (2021) · FEBS Open Bio · doi:10.1002/2211-5463.13110 · Cited by 183

Cryo-EM structure of the human cardiac myosin filament

Dutta, D., Nguyen, V., Campbell, K. S., Padrón, R., & Craig, R. (2023) · Nature · doi:10.1038/s41586-023-06691-4 · Cited by 164

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · doi:10.1101/2021.09.26.461876 · Cited by 122

Design principles for cyclin K molecular glue degraders

Kozicka, Z., Suchyta, D. J., Focht, V., Kempf, G., Petzold, G., Jentzsch, M., Zou, C., Di Genua, C., Donovan, K. A., Coomar, S., et al. (2024) · Nature Chemical Biology · doi:10.1038/s41589-023-01409-z · Cited by 113

A hold-and-feed mechanism drives directional DNA loop extrusion by condensin

Shaltiel, I. A., Datta, S., Lecomte, L., Hassler, M., Kschonsak, M., Bravo, S., Stober, C., Ormanns, J., Eustermann, S., & Haering, C. H. (2022) · Science · doi:10.1126/science.abm4012 · Cited by 112

The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA

Deep, A., Gu, Y., Gao, Y.-Q., Ego, K. M., Herzik, M. A., Zhou, H., & Corbett, K. D. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.008 · Cited by 106

Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes

Killer, M., Wald, J., Pieprzyk, J., Marlovits, T. C., & Löw, C. (2021) · Science Advances · doi:10.1126/sciadv.abk3259 · Cited by 94

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome

Healy, M. D., McNally, K. E., Butkovič, R., Chilton, M., Kato, K., Sacharz, J., McConville, C., Moody, E. R. R., Shaw, S., Planelles-Herrero, V. J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.003 · Cited by 91

Fusion protein strategies for cryo-EM study of G protein-coupled receptors

Zhang, K., Wu, H., Hoppe, N., Manglik, A., & Cheng, Y. (2022) · Nature Communications · doi:10.1038/s41467-022-32125-2 · Cited by 91

How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication

Jones, M. L., Aria, V., Baris, Y., & Yeeles, J. T. P. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.035 · Cited by 86

Structural basis for membrane attack complex inhibition by CD59

Couves, E. C., Gardner, S., Voisin, T. B., Bickel, J. K., Stansfeld, P. J., Tate, E. W., & Bubeck, D. (2023) · Nature Communications · doi:10.1038/s41467-023-36441-z · Cited by 85

The structure of an Hsp90-immunophilin complex reveals cochaperone recognition of the client maturation state

Lee, K., Thwin, A. C., Nadel, C. M., Tse, E., Gates, S. N., Gestwicki, J. E., & Southworth, D. R. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.023 · Cited by 76

Structural basis of BRCC36 function in DNA repair and immune regulation

Rabl, J., Bunker, R. D., Schenk, A. D., Cavadini, S., Gill, M. E., Abdulrahman, W., Andrés-Pons, A., Luijsterburg, M. S., Ibrahim, A. F. M., Branigan, E., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.002 · Cited by 84

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes

Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G., Bouhaddou, M., Fossati, A., Brilot, A. F., et al. (2021) · doi:10.1101/2021.05.10.443524 · Cited by 89

IFT-A structure reveals carriages for membrane protein transport into cilia

Hesketh, S. J., Mukhopadhyay, A. G., Nakamura, D., Toropova, K., & Roberts, A. J. (2022) · Cell · doi:10.1016/j.cell.2022.11.010 · Cited by 83

Molecular basis of proton sensing by G protein-coupled receptors

Howard, M. K., Hoppe, N., Huang, X.-P., Mitrovic, D., Billesbølle, C. B., Macdonald, C. B., Mehrotra, E., Rockefeller Grimes, P., Trinidad, D. D., Delemotte, L., et al. (2025) · Cell · doi:10.1016/j.cell.2024.11.036 · Cited by 77

Structure of human PINK1 at a mitochondrial TOM-VDAC array

Callegari, S., Kirk, N. S., Gan, Z. Y., Dite, T., Cobbold, S. A., Leis, A., Dagley, L. F., Glukhova, A., & Komander, D. (2025) · Science · doi:10.1126/science.adu6445 · Cited by 75

UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability

Tsai, J. M., Aguirre, J. D., Li, Y.-D., Brown, J., Focht, V., Kater, L., Kempf, G., Sandoval, B., Schmitt, S., Rutter, J. C., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.028 · Cited by 68

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

Park, Y.-J., Pinto, D., Walls, A. C., Liu, Z., De Marco, A., Benigni, F., Zatta, F., Silacci-Fregni, C., Bassi, J., Sprouse, K. R., et al. (2022) · doi:10.1101/2022.05.08.491108 · Cited by 251

Cryo-EM structure of gas vesicles for buoyancy-controlled motility

Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D., & Jakobi, A. J. (2023) · Cell · doi:10.1016/j.cell.2023.01.041 · Cited by 62

Cryo-EM and artificial intelligence visualize endogenous protein community members

Skalidis, I., Kyrilis, F. L., Tüting, C., Hamdi, F., Chojnowski, G., & Kastritis, P. L. (2022) · Structure · doi:10.1016/j.str.2022.01.001 · Cited by 61

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Pezeshkian, W., Grünewald, F., Narykov, O., Lu, S., Arkhipova, V., Solodovnikov, A., Wassenaar, T. A., Marrink, S. J., & Korkin, D. (2023) · Structure · doi:10.1016/j.str.2023.02.006 · Cited by 60

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles

Coupland, C. E., Karimi, R., Bueler, S. A., Liang, Y., Courbon, G. M., Di Trani, J. M., Wong, C. J., Saghian, R., Youn, J.-Y., Wang, L.-Y., et al. (2024) · Science · doi:10.1126/science.adp5577 · Cited by 58

Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia

Gong, R., Jiang, F., Moreland, Z. G., Reynolds, M. J., de los Reyes, S. E., Gurel, P., Shams, A., Heidings, J. B., Bowl, M. R., Bird, J. E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abl4733 · Cited by 56

Structural basis for Parkinson’s disease-linked LRRK2’s binding to microtubules

Snead, D. M., Matyszewski, M., Dickey, A. M., Lin, Y. X., Leschziner, A. E., & Reck-Peterson, S. L. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00863-y · Cited by 54

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat

Nishio, S., Emori, C., Wiseman, B., Fahrenkamp, D., Dioguardi, E., Zamora-Caballero, S., Bokhove, M., Han, L., Stsiapanava, A., Algarra, B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.013 · Cited by 54

Cryptochrome–Timeless structure reveals circadian clock timing mechanisms

Lin, C., Feng, S., DeOliveira, C. C., & Crane, B. R. (2023) · Nature · doi:10.1038/s41586-023-06009-4 · Cited by 51

Structure of ATP synthase under strain during catalysis

Guo, H., & Rubinstein, J. L. (2022) · Nature Communications · doi:10.1038/s41467-022-29893-2 · Cited by 51

STK19 positions TFIIH for cell-free transcription-coupled DNA repair

Mevissen, T. E. T., Kümmecke, M., Schmid, E. W., Farnung, L., & Walter, J. C. (2024) · Cell · doi:10.1016/j.cell.2024.10.020 · Cited by 50

Clamping of DNA shuts the condensin neck gate

Lee, B.-G., Rhodes, J., & Löwe, J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2120006119 · Cited by 49

Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases

Hunkeler, M., Jin, C. Y., & Fischer, E. S. (2023) · Science · doi:10.1126/science.ade5750 · Cited by 48

Structure and interactions of the endogenous human Commander complex

Laulumaa, S., Kumpula, E.-P., Huiskonen, J. T., & Varjosalo, M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01246-1 · Cited by 46

High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

Ouyang, R., Costa, A. R., Cassidy, C. K., Otwinowska, A., Williams, V. C. J., Latka, A., Stansfeld, P. J., Drulis-Kawa, Z., Briers, Y., Pelt, D. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34972-5 · Cited by 46

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

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The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice

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The structure of apolipoprotein B100 from human low-density lipoprotein

Berndsen, Z. T., & Cassidy, C. K. (2025) · Nature · doi:10.1038/s41586-024-08467-w · Cited by 43

Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation

Jansen, R. M., Peruzzo, R., Fromm, S. A., Yokom, A. L., Zoncu, R., & Hurley, J. H. (2022) · Science Advances · doi:10.1126/sciadv.add2926 · Cited by 42

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13

Kim, S. K., Dickinson, M. S., Finer-Moore, J., Guan, Z., Kaake, R. M., Echeverria, I., Chen, J., Pulido, E. H., Sali, A., Krogan, N. J., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00918-0 · Cited by 41

Structural basis for human mitochondrial tRNA maturation

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Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex

(2025) · doi:10.1038/s41594-025-01557-x · Cited by 40

Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling

Qi, X., Hu, Q., Elghobashi-Meinhardt, N., Long, T., Chen, H., & Li, X. (2023) · Cell · doi:10.1016/j.cell.2023.09.021 · Cited by 40

Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament

Liu, T., Cao, L., Mladenov, M., Jegou, A., Way, M., & Moores, C. A. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01205-2 · Cited by 40

The PfRCR complex bridges malaria parasite and erythrocyte during invasion

Farrell, B., Alam, N., Hart, M. N., Jamwal, A., Ragotte, R. J., Walters-Morgan, H., Draper, S. J., Knuepfer, E., & Higgins, M. K. (2024) · Nature · doi:10.1038/s41586-023-06856-1 · Cited by 39

The structure of HiSiaQM defines the architecture of tripartite ATP-independent periplasmic (TRAP) transporters

Peter, M. F., Depping, P., Schneberger, N., Severi, E., Gatterdam, K., Tindall, S., Durand, A., Heinz, V., Koenig, P.-A., Geyer, M., et al. (2021) · doi:10.1101/2021.12.03.471092 · Cited by 38

Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter

Peter, M. F., Ruland, J. A., Depping, P., Schneberger, N., Severi, E., Moecking, J., Gatterdam, K., Tindall, S., Durand, A., Heinz, V., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31907-y · Cited by 38

Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation

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Broadly inhibitory antibodies to severe malaria virulence proteins

Reyes, R. A., Raghavan, S. S. R., Hurlburt, N. K., Introini, V., Bol, S., Kana, I. H., Jensen, R. W., Martinez-Scholze, E., Gestal-Mato, M., López-Gutiérrez, B., et al. (2024) · Nature · doi:10.1038/s41586-024-08220-3 · Cited by 35

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

Vuckovic, Z., Wang, J., Pham, V., Mobbs, J. I., Belousoff, M. J., Bhattarai, A., Burger, W. A., Thompson, G., Yeasmin, M., Nawaratne, V., et al. (2023) · eLife · doi:10.7554/elife.83477 · Cited by 34

Structural basis for plasmid restriction by SMC JET nuclease

Roisné-Hamelin, F., Liu, H. W., Taschner, M., Li, Y., & Gruber, S. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.01.009 · Cited by 34

Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules

Muir, K. W., Batters, C., Dendooven, T., Yang, J., Zhang, Z., Burt, A., & Barford, D. (2023) · Science · doi:10.1126/science.adj8736 · Cited by 34

Structural pathway for PI3-kinase regulation by VPS15 in autophagy

Cook, A. S. I., Chen, M., Nguyen, T. N., Cabezudo, A. C., Khuu, G., Rao, S., Garcia, S. N., Yang, M., Iavarone, A. T., Ren, X., et al. (2025) · Science · doi:10.1126/science.adl3787 · Cited by 34

Structural conservation of insulin/IGF signalling axis at the insulin receptors level in Drosophila and humans

Viola, C. M., Frittmann, O., Jenkins, H. T., Shafi, T., De Meyts, P., & Brzozowski, A. M. (2023) · Nature Communications · doi:10.1038/s41467-023-41862-x · Cited by 34

Visualizing chaperone-mediated multistep assembly of the human 20S proteasome

Adolf, F., Du, J., Goodall, E. A., Walsh, R. M., Rawson, S., von Gronau, S., Harper, J. W., Hanna, J., & Schulman, B. A. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01268-9 · Cited by 33

Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III

Di Trani, J. M., Liu, Z., Whitesell, L., Brzezinski, P., Cowen, L. E., & Rubinstein, J. L. (2022) · Structure · doi:10.1016/j.str.2021.08.006 · Cited by 32

Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases

Sokratian, A., Zhou, Y., Tatli, M., Burbidge, K. J., Xu, E., Viverette, E., Donzelli, S., Duda, A. M., Yuan, Y., Li, H., et al. (2024) · Science Advances · doi:10.1126/sciadv.adq3539 · Cited by 32

The kidney slit diaphragm resembles a fishnet

Birtasu, A. N., Wieland, K., Ermel, U. H., Arghittu, S. M., Manger, S., Kocylowski, M. K., Fakler, B., Scheffer, M. P., Covino, R., Grahammer, F., et al. (2025) · Kidney International · doi:10.1016/j.kint.2025.08.028 · Cited by 32

A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability

Podgorski, J. M., Freeman, K., Gosselin, S., Huet, A., Conway, J. F., Bird, M., Grecco, J., Patel, S., Jacobs-Sera, D., Hatfull, G., et al. (2023) · Structure · doi:10.1016/j.str.2022.12.012 · Cited by 32

The structural basis for RNA slicing by human Argonaute2

Mohamed, A. A., Wang, P. Y., Bartel, D. P., & Vos, S. M. (2025) · Cell Reports · doi:10.1016/j.celrep.2024.115166 · Cited by 32

Structure and design of Langya virus glycoprotein antigens

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Structure of mycobacterial respiratory complex I

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