cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Cited by (153)

Items 101–153 of 153

1. Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation
   Jette, Claudia A., Barnes, Christopher O., Kirk, Sharon M., Melillo, Bruno, Smith, Amos B., Bjorkman, Pamela J. · 2021 · Nature Communications
2. Structure of a P element transposase–DNA complex reveals unusual DNA structures and GTP-DNA contacts
   Ghanim, George E., Kellogg, Elizabeth H., Nogales, Eva, Rio, Donald C. · 2019 · Nature Structural & Molecular Biology
3. Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer
   Wilson, Marcus D., Renault, Ludovic, Maskell, Daniel P., Ghoneim, Mohamed, Pye, Valerie E., Nans, Andrea, Rueda, David S., Cherepanov, Peter, Costa, Alessandro · 2019 · Nature Communications
4. Filling Adeno-Associated Virus Capsids: Estimating Success by Cryo-Electron Microscopy
   Subramanian, Suriyasri, Maurer, Anna C., Bator, Carol M., Makhov, Alexander M., Conway, James F., Turner, Kevin B., Marden, James H., Vandenberghe, Luk H., Hafenstein, Susan L. · 2019 · Human Gene Therapy
5. Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies
   Muecksch, Frauke, Weisblum, Yiska, Barnes, Christopher O., Schmidt, Fabian, Schaefer-Babajew, Dennis, Lorenzi, Julio C C, Flyak, Andrew I, DeLaitsch, Andrew T, Huey-Tubman, Kathryn E, Hou, Shurong et al. · 2021
6. An adeno-associated virus variant enabling efficient ocular-directed gene delivery across species
   Luo, Shuang, Jiang, Hao, Li, Qingwei, Qin, Yingfei, Yang, Shiping, Li, Jing, Xu, Lingli, Gou, Yan, Zhang, Yafei, Liu, Fengjiang et al. · 2024 · Nature Communications
7. The structure of HiSiaQM defines the architecture of tripartite ATP-independent periplasmic (TRAP) transporters
   Peter, Martin F., Depping, Peer, Schneberger, Niels, Severi, Emmanuele, Gatterdam, Karl, Tindall, Sarah, Durand, Alexandre, Heinz, Veronika, Koenig, Paul-Albert, Geyer, Matthias et al. · 2021
8. Structural basis of substrate recognition and translocation by human very long-chain fatty acid transporter ABCD1
   Chen, Zhi-Peng, Xu, Da, Wang, Liang, Mao, Yao-Xu, Li, Yang, Cheng, Meng-Ting, Zhou, Cong-Zhao, Hou, Wen-Tao, Chen, Yuxing · 2022 · Nature Communications
9. Structural basis for plasmid restriction by SMC JET nuclease
   Roisné-Hamelin, Florian, Liu, Hon Wing, Taschner, Michael, Li, Yan, Gruber, Stephan · 2024 · Molecular Cell
10. Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III
    Di Trani, Justin M., Liu, Zhongle, Whitesell, Luke, Brzezinski, Peter, Cowen, Leah E., Rubinstein, John L. · 2022 · Structure
11. Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex
    Wan, Mandy S. M., Muhammad, Reyhan, Koliopoulos, Marios G., Roumeliotis, Theodoros I., Choudhary, Jyoti S., Alfieri, Claudio · 2023 · Nature Communications
12. Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ
    Barski, Michał S., Minnell, Jordan J., Hodakova, Zuzana, Pye, Valerie E., Nans, Andrea, Cherepanov, Peter, Maertens, Goedele N. · 2020 · Nature Communications
13. Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake
    Long, Tao, Li, Dongyu, Vale, Goncalo, Jiang, Yaoyukun, Schmiege, Philip, Yang, Zhongyue J., McDonald, Jeffrey G., Li, Xiaochun · 2024 · Cell
14. Structures of tweety homolog proteins TTYH2 and TTYH3 reveal a Ca2+-dependent switch from intra- to intermembrane dimerization
    Li, Baobin, Hoel, Christopher M., Brohawn, Stephen G. · 2021 · Nature Communications
15. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation
    Harrison, Jerry Joe E. K., Passos, Dario Oliveira, Bruhn, Jessica F., Bauman, Joseph D., Tuberty, Lynda, DeStefano, Jeffrey J., Ruiz, Francesc Xavier, Lyumkis, Dmitry, Arnold, Eddy · 2022 · Science Advances
16. Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection
    Guo, Yu, Zhang, Guangshun, Yang, Qi, Xie, Xiaowei, Lu, Yang, Cheng, Xuelian, Wang, Hui, Liang, Jingxi, Tang, Jielin, Gao, Yuxin et al. · 2023 · Nature Communications
17. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism
    Lomakin, Ivan B, Devarkar, Swapnil C, Patel, Shivali, Grada, Ayman, Bunick, Christopher G · 2023 · Nucleic Acids Research
18. Molecular basis of FIGNL1 in dissociating RAD51 from DNA and chromatin
    Carver, Alexander, Yu, Tai-Yuan, Yates, Luke A., White, Travis, Wang, Raymond, Lister, Katie, Jasin, Maria, Zhang, Xiaodong · 2025 · Science
19. Structural diversity and clustering of bacterial flagellar outer domains
    Fields, Jessie Lynda, Zhang, Hua, Bellis, Nathan F., Petersen, Holly A., Halder, Sajal K., Rich-New, Shane T., Krupovic, Mart, Wu, Hui, Wang, Fengbin · 2024 · Nature Communications
20. A cereblon-based glue degrader of NEK7 regulates NLRP3 inflammasome in a context-dependent manner
    Sylvain, Aude, Stoehr, Natacha, Ma, Fupeng, Cernijenko, Artiom, Schröder, Martin, Khoshouei, Maryam, Vogelsanger, Melanie, Schoenboerner, Michel, Burke, Ashley, Rao, Pasupuleti et al. · 2025 · Cell Chemical Biology
21. Structural basis for Retriever-SNX17 assembly and endosomal sorting
    Singla, Amika, Boesch, Daniel J., Fung, Ho Yee Joyce, Ngoka, Chigozie, Enriquez, Avery S., Song, Ran, Kramer, Daniel A., Han, Yan, Banarer, Esther, Lemoff, Andrew et al. · 2024 · Nature Communications
22. PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation
    Dhingra, Yukti, Suresh, Shravanti K., Juneja, Puneet, Sashital, Dipali G. · 2022 · Molecular Cell
23. Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline
    Li, Xiang, Wang, Mengjiao, Denk, Timo, Buschauer, Robert, Li, Yi, Beckmann, Roland, Cheng, Jingdong · 2024 · Nature Communications
24. A Peptide Derived from Lens Epithelium–Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies
    Li, Min, Chen, Xuemin, Wang, Huaibin, Jurado, Kellie A., Engelman, Alan N., Craigie, Robert · 2020 · Journal of Molecular Biology
25. Predicting the conformational flexibility of antibody and T-cell receptor CDRs
    Spoendlin, Fabian C., Fernández-Quintero, Monica L., Raghavan, Sai S. R., Turner, Hannah L., Gharpure, Anant, Loeffler, Johannes R., Wong, Wing K., Bujotzek, Alexander, Georges, Guy, Ward, Andrew B. et al. · 2025
26. The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics
    Llerena Schiffmacher, Diana A., Lee, Shun-Hsiao, Kliza, Katarzyna W., Theil, Arjan F., Akita, Masaki, Helfricht, Angela, Bezstarosti, Karel, Gonzalo-Hansen, Camila, van Attikum, Haico, Verlaan-de Vries, Matty et al. · 2024 · Nature Communications
27. HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro
    Li, Min, Yang, Renbin, Chen, Xuemin, Wang, Huaibin, Ghirlando, Rodolfo, Dimitriadis, Emilios.K., Craigie, Robert · 2024 · Journal of Molecular Biology
28. Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome
    Pandey, Krishan K., Bera, Sibes, Shi, Ke, Rau, Michael J., Oleru, Amarachi V., Fitzpatrick, James A. J., Engelman, Alan N., Aihara, Hideki, Grandgenett, Duane P. · 2021 · Communications Biology
29. T cell toxicity induced by tigecycline binding to the mitochondrial ribosome
    Shao, Qiuya, Khawaja, Anas, Nguyen, Minh Duc, Singh, Vivek, Zhang, Jingdian, Liu, Yong, Nordin, Joel, Adori, Monika, Axel Innis, C., Castro Dopico, Xaquin et al. · 2025 · Nature Communications
30. Cryo-EM reveals the conformational epitope of human monoclonal antibody PAM1.4 broadly reacting with polymorphic malarial protein VAR2CSA
    Raghavan, Sai Sundar Rajan, Dagil, Robert, Lopez-Perez, Mary, Conrad, Julian, Bassi, Maria Rosaria, Quintana, Maria del Pilar, Choudhary, Swati, Gustavsson, Tobias, Wang, Yong, Gourdon, Pontus et al. · 2022 · PLOS Pathogens
31. Phosphorylation-mediated conformational change regulates human SLFN11
    Kugler, Michael, Metzner, Felix J., Witte, Gregor, Hopfner, Karl-Peter, Lammens, Katja · 2024 · Nature Communications
32. Spatial N-glycan rearrangement on α5β1 integrin nucleates galectin-3 oligomers to determine endocytic fate
    Shafaq-Zadah, Massiullah, Dransart, Estelle, Hamitouche, Ilyes, Wunder, Christian, Chambon, Valérie, Valades-Cruz, Cesar A., Leconte, Ludovic, Sarangi, Nirod Kumar, Robinson, Jack, Bai, Siau-Kun et al. · 2025 · Nature Communications
33. Cryo-EM structure of the human Asc-1 transporter complex
    Li, Yaning, Guo, Yingying, Bröer, Angelika, Dai, Lu, Brӧer, Stefan, Yan, Renhong · 2024 · Nature Communications
34. High-affinity PQQ import is widespread in Gram-negative bacteria
    Munder, Fabian, Voutsinos, Marcos, Hantke, Klaus, Venugopal, Hari, Grinter, Rhys · 2025 · Science Advances
35. The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins
    Körner, Carolin, Schäfer, Jan-Hannes, Esch, Bianca M., Parey, Kristian, Walter, Stefan, Teis, David, Januliene, Dovile, Schmidt, Oliver, Moeller, Arne, Fröhlich, Florian · 2024 · Cell Reports
36. Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius
    Furlanetto, Valentina, Kalyani, Dayanand C., Kostelac, Anja, Puc, Jolanta, Haltrich, Dietmar, Hällberg, B. Martin, Divne, Christina · 2024 · Journal of Molecular Biology
37. Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin
    Lomakin, Ivan B., Devarkar, Swapnil C., Grada, Ayman, Bunick, Christopher G. · 2024 · Journal of Investigative Dermatology
38. The crystal and cryo-EM structures of PLCγ2 reveal dynamic interdomain recognitions in autoinhibition
    Shin, Young-Cheul, Plummer-Medeiros, Ashlee Marie, Mungenast, Alison, Choi, Hyeong-wook, TenDyke, Karen, Zhu, Xiaojie, Shepard, Jennifer, Sanders, Kristen, Zhuang, Ningning, Hu, Liang et al. · 2024 · Science Advances
39. Cryo-EM structure of native honey bee vitellogenin
    Montserrat-Canals, Mateu, Schnelle, Kilian, Leipart, Vilde, Halskau, Øyvind, Amdam, Gro V., Moeller, Arne, Cunha, Eva S., Luecke, Hartmut · 2025 · Nature Communications
40. Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
    Fraser, Alec, Sokolova, Maria L., Drobysheva, Arina V., Gordeeva, Julia V., Borukhov, Sergei, Jumper, John, Severinov, Konstantin V., Leiman, Petr G. · 2022 · Nature Communications
41. Molecular mechanism of PP2A/B55α phosphatase inhibition by IER5
    Cao, Ruili, Jones, Daniel T.D., Pan, Li, Yang, Annie, Wang, Shumei, Padi, Sathish K.R., Rawson, Shaun, Aster, Jon C., Blacklow, Stephen C. · 2025 · Cell Chemical Biology
42. Cryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase
    Yang, Xiaoli, Ding, Zhanyu, Peng, Lisi, Song, Qiuyue, Zhang, Deyu, Cui, Fang, Xia, Chuanchao, Li, Keliang, Yin, Hua, Li, Shiyu et al. · 2022 · Nature Communications
43. Molecular insights into human phosphatidylserine synthase 2 and its regulation of SREBP pathways
    Li, Dongyu, Chen, Hongwen, Vale, Goncalo, Elghobashi-Meinhardt, Nadia, Hatton, Alexandra, Rong, Shunxing, McDonald, Jeffrey G., Li, Xiaochun · 2025 · Proceedings of the National Academy of Sciences
44. Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology
    Piccoli, Luca, Park, Young-Jun, Tortorici, M. Alejandra, Czudnochowski, Nadine, Walls, Alexandra C., Beltramello, Martina, Silacci-Fregni, Chiara, Pinto, Dora, Rosen, Laura E., Bowen, John E. et al. · 2020 · Cell
45. Structural basis for Salmonella infection by two Microviridae phages
    Hu, Wanlong, Liu, Zhengjie, Wei, Yuming, Bian, Qucheng, Lan, Weiqi, Fan, Chongzheng, Song, Jiaoyang, Sun, Qianqian, Zhang, Xiaojie, Liu, Yuqing et al. · 2025 · Communications Biology
46. Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus
    Burmeister, Wim P., Boutin, Laetitia, Balestra, Aurelia C., Gröger, Henri, Ballandras-Colas, Allison, Hutin, Stephanie, Kraft, Christian, Grimm, Clemens, Böttcher, Bettina, Fischer, Utz et al. · 2024 · PLOS Pathogens
47. Dual site targeting of the bacterial 70S ribosome by tetracyclines
    Devarkar, Swapnil C., Lomakin, Ivan B., Wang, Jimin, Grada, Ayman, Bunick, Christopher G. · 2026 · Nature Communications
48. ApoE is Secreted as a Lipid Nanoparticle by Mammalian Cells: Implications for Alzheimer’s Disease Pathogenesis
    Hernandez Arriaza, Ricardo, Reil, Dylan, Fatuzzo, Nina, Fu, Mengying, Dai, Yuqin, Fernandez Martinez, David, Jiang, Hong, Holtzman, David M., Greicius, Michael D., Khosla, Chaitan · 2025 · Biochemistry
49. Engineering a compact high-fidelity Staphylococcus aureus Cas9 variant with broader targeting range and mechanistic insights into its activation
    Omura, Satoshi N., Nakagawa, Ryoya, Kajimoto, Shohei, Okazaki, Sae, Ishiguro, Soh, Mori, Hideto, Onishi, Kosuke, Kashiwakura, Yuji, Hiramoto, Takafumi, Horinaka, Kio et al. · 2026 · Nature Communications
50. Extensive natural variation in bacterial ribosomal drug-binding sites
    Ekemezie, Chinenye L., Chan, Lewis I., Brown, Charlotte R., Helena-Bueno, Karla, Williams, Tom A., Melnikov, Sergey V. · 2025 · Cell Reports
51. Amino acid and viral binding by the high-affinity Cationic Amino acid Transporter 1 (CAT1) from Mus musculus
    Ye, Mingda, Liang, Zhu, Zhou, Daming, Pike, Ashley C. W., Wang, SiYi, Wang, Dong, Bakshi, Souvika, Brooke, Laurent, Williams, Eleanor P., Elkins, Jonathan M. et al. · 2026 · Nature Communications
52. Taxane-induced conformational changes in the microtubule lattice activate GEF-H1-dependent RhoA signalling
    Meiring, Joyce C. M., Mahapatra, Varsha, Liu, Ruijie, Gravett, Molly S. C., Morren, Daan, Saunders, Harriet A. J., Choi, Sung Ryul, Pelster José, Andressa, Karhanova, Adela, Metallidou, Ioanna et al. · 2026 · Nature Cell Biology
53. Structural and mechanistic insights into the constitutive Themis–Grb2 complex in T cell signalling
    Clancy, Danielle M., Sanz-Sanjuan, Alba, Gilis, Elisabeth, Tougaard, Peter, Velghe, Imke, Van Droogenbroeck, Yana, Felix, Jan, Bloch, Yehudi, Cuadrado, Álvaro Furones, Merceron, Romain et al. · 2026 · Nature Communications