Through cryo-electron tomography (Cryo-ET) analysis, it was confirmed that wild-type S. acidocaldarius accumulates intracellular glycogen, whereas the ΔAmyA mutant is deficient in glycogen.
Lee A, Park N, Song C & Cha J (2025) AmyA contributes to the glycogen synthesis in Sulfolobus acidocaldarius. Int J Biol Macromol, 141431.
Oxyrrhis marina is a unicellular protist with a unique nucleus in which chromosomes are always present throughout the entire cell cycle, making it an important subject of evolutionary studies. Chromosomes within the nucleus of Oxyrrhis marina were three-dimensionally reconstructed using serial sectioning and SBF-SEM–based volume imaging techniques.
Fukuda Y, Suzaki T, Murata K & Song C (2025) Novel ultrastructural features of the nucleus of the ancestral dinoflagellate Oxyrrhis marina as revealed by freeze substitution fixation. Front Protistol 3, 1512258.
The structural polymorphism of amyloid-β (Aβ) fibrils plays a crucial role in the pathology of Alzheimer’s disease (AD), but the mechanisms underlying this diversity remain poorly understood. In this study, we identified a novel J-shaped protomer structure of Aβ40 fibrils and resolved it at 3.3 Å resolution using cryo-EM helical reconstruction.
Burton-Smith RN, Yagi-Utsumi M, Yanaka S, Song C, Murata K & Kato K (2025) Elucidating the Unique J-Shaped Protomer Structure of Amyloid-β(1-40) Fibril with Cryo-Electron Microscopy. Int J Mol Sci 26(3), 1179.
The adhesive function of cell surface proteins can be visually assessed through direct observation; however, the structural elements mediating adhesion are invisible at the nanoscale, limiting our understanding of the molecular diversity underlying cell–cell adhesion. Analysis of DNA origami nanoblocks using transmission electron microscopy (TEM) and high-speed atomic force microscopy (AFM) revealed a hinge structure that separates the membrane-distal and membrane-proximal regions.
Oda H, Nishiguchi S, Song C, Murata K, Uchihashi T & Suzuki Y (2025) Nanoscale visualization of Drosophila E-cadherin ectodomain fragments and their interactions using DNA origami nanoblocks. Journal of Molecular Biology, 437(2), 168875.
Single-particle 3D reconstruction based on electron microscopy (EM) revealed that gelsolin undergoes subtle structural changes in the presence of calcium prior to binding actin.
Kim HU, Park YH, An, MY, Kim, YK, Song C & Jung HS (2024) Structural insights into calcium-induced conformational changes in human gelsolin. Biochemical and Biophysical Research Communications, 735, 150826.
Nitrification is a key process in the global nitrogen (N) cycle, mediated by ammonia-oxidizing microorganisms, with ammonia-oxidizing archaea (AOA) playing a particularly important role. Cryo-electron tomography (Cryo-ET) analysis revealed that the S-layer structure, which is observed in conventional AOAs, is absent on the cell exterior of Nitrosocosmicus AOA.
Han S, Kim S, Sedlacek C J, Farooq A, Song C, Lee S, Liu S, Brüggemann N, Rohe L, Kwon M, Rhee S K & Jung M Y (2024) Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea. Mbio, 15(11), e02169-24.
The structural determination of large π-conjugated molecules using microcrystal electron diffraction (MicroED) has been demonstrated. Poorly soluble tweezer-shaped molecular solids were directly analyzed by MicroED in the reaction vessel to elucidate their structures and assembly modes. This study validates the efficiency of MicroED for the structural determination of such compounds.
Sugiyama H, Watanabe K, Song C, Murata K & Segawa Y (2024) Structure Determination of Tweezer-shaped π-Extended Tetraphenylenes without Recrystallization by Microcrystal Electron Diffraction. Chemical Letters 53, upae192.
Medusavirus is a giant virus belonging to the family Mamonoviridae, and infected amoebae release not only mature virions but also immature particles. However, the capsid structure during viral maturation remains unknown. In this study, we applied a block-based reconstruction approach in cryo-EM single-particle analysis to resolve the structure at 7–10 Å resolution.
Watanabe R, Song C, Takemura T & Murata K (2024) Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy. J Virol 98(9), e0043624.
The anti-cancer therapeutic IgG, Rituximab, was analyzed by phase plate single-particle cryo-EM to investigate its structural conformations in solution. This study revealed the structural heterogeneity of IgG and demonstrated the utility of phase plates for cryo-EM analysis of small asymmetric proteins. It is anticipated to be the last historical study using a Zernike phase plate (a phase plate with a central hole), rather than a Volta phase plate.
Lin SSY, Kato T, Namba K, Hosogi N, Song C, Murata K, Yen CH, Hsu TL, Wong CH, Wu YM, Tu IP & Chang WH (2024) Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å. Sci Rep 14, 14079.
The vacuolar-type ATPase (EhV-ATPase) from Enterococcus hirae is a unique V-ATPase variant that performs Na⁺ transport and possesses an off-axis rotor. Using ATP to activate the EhV-ATPase complex, cryo-EM single-particle analysis resolved a total of six structural states.
Burton-Smith RN, Song C, Ueno H, Murata T, Iino R & Murata K (2023) Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover Comm Biol 6, 755.
Negeviruses are recently discovered viruses that infect insects and are phylogenetically related to certain plant viruses. They possess a unique virion structure with an elliptical core and short projections. Here, we performed the first cryo-EM single-particle analysis of Tanay virus (TANAV), a member of the negevirus group.
Okamoto K, Song C, Wang H, Sakaguchi M, Chalkiadaki C, Miyazaki N, Nabeshima T, Morita K, Inoue S & Murata K (2023) Structure and its transformation of elliptical nege-like virus Tanay virus. J Gen Virol. 104(6), 001863
Mitophagy plays a crucial role in maintaining mitochondrial homeostasis through the selective degradation of mitochondria. During mitophagy, mitochondrial fission is required for engulfment by autophagosomes; however, the canonical mitochondrial fission factor Dnm1 (DNM1L/Drp1) is not essential for mitophagy. In this study, we identified a novel mitochondrial fission factor, Atg44, which is essential for mitophagy in yeast, and named it mitofissin. Wild-type S. cerevisiae and atg44Δ cells were collected and subjected to volume imaging using FIB-SEM.
Fukuda T, Furukawa K, Maruyama T, Yamashita SI, Noshiro D, Song C, Ogasawara Y, Okuyama K, Alam JM, Hayatsu M, Saigusa T, Inoue K, Ikeda K, Takai A, Chen L, Lahiri V, Okada Y, Shibata S, Murata K, Klionsky DJ, Noda NN & Kanki T (2023) The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy. Mol Cell 83(12), 2045-2058.e9.
Ostreococcus tauri is a model green alga used for studying the light-harvesting systems of photosynthesis. In this study, we analyzed the PSI supercomplex structure under low-light conditions using cryo-EM single-particle analysis and confirmed that it associates with LHCI and Lhcp to enhance light-harvesting capacity.
Ishii A, Shan J, Sheng X, Kim E, Watanabe A, Yokono M, Noda C, Song C, Murata K, Liu Z & Minagawa J (2023) The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers. Elife 12, e84488.