2023
P. Artigas, D. J. Meyer, V. C. Young, K. Spontarelli, J. Eastman, E. Strandquist, H. Rui, B. Roux, M. A. Birk, H. Nakanishi, K. Abe, C. Gatto (2023) A Na pump with reduced stoichiometry is up-regulated by brine shrimp in extreme salinities. Proc. Natl. Acad. Sci. U.S.A. 120(52)e2313999120. doi: 10.1073/pnas.2313999120
Pub Med
Open Access
H. V. Madapally, K. Abe, V. Dubey, H. Khandelia (2023) Specific protonation of acidic residues confers K+ selectivity to the gastric proton pump. J. Biol. Chem. 8:105542. doi: 10.1016/j.jbc.2023.105542
Pub Med
Open Access
S. Suzuki, K. Tanaka, K. Nishikawa, H. Suzuki, A. Oshima, Y. Fujiyoshi (2023) Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding. Nat. Commun. 14:5899. doi: 10.1038/s41467-023-41650-7
Pub Med
Open Access
K. Abe, M. Ozako, M. Inukai, Y. Matsuyuki, S. Kitayama, C. Kanai, C. Nagai, C. C. Gopalasingam, C. Gerle, H. Shigematsu, N. Umekubo, S. Yokoshima, A. Yoshimori (2023) Deep learning driven de novo drug design based on gastric proton pump structures. Commun. Biol. 6:956. doi: 10.1038/s42003-023-05334-8
Pub Med
Open Access
Press Release
K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi (2023) The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat. Commun. 14(1):4236. doi: 10.1038/s41467-023-39987-0
Pub Med
Open Access
Press Release
K. Abe, T. Nishizawa, P. Artigas (2023) An unusual conformation from Na+-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na+-binding. Biochim. Biophys. Acta, Mol. Cell Res. doi: 10.1016/j.bbamcr.2023.119543
Pub Med
Open Access
C. Gerle, Y. Misumi, A. Kawamoto, H. Tanaka, H. Kawai-Kubota, R. Tokutsu, E. Kim, D. Chorev, K. Abe, C.V. Robinson, K. Mitsuoka, J. Minagawa, G. Kurisu (2023) Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin. Biochim. Biophys. Acta–Bioenergetics. doi: 10.1016/j.bbabio.2023.148986
Pub Med
Open Access
D. Kozai, N. Numoto, K. Nishikawa, A. Kamegawa, S. Kawasaki, Y. Hiroaki, K. Irie, A. Oshima, H. Hanzawa, K. Shimada, Y. Kitano, Y. Fujiyoshi (2023) Recognition mechanism of a novel gabapentinoid drug, mirogabalin, for recombinant human α2δ1, a voltage-gated calcium channel subunit. J. Mol. Biol. doi: 10.1016/j.jmb.2023.168049
Pub Med
Open Access
2022
V. C. Young, H. Nakanishi, D. J. Meyer, T. Nishizawa, A. Oshima, P. Artigas, K. Abe (2022) Structure and function of H+/K+ pump mutants reveal Na+/K+ pump mechanisms. Nat. Commun. 13:5270. doi: 10.1038/s41467-022-32793-0
Pub Med
Open Access
S. Suzuki, M. Iida, Y. Hiroaki, K. Tanaka, A. Kawamoto, T. Kato, A. Oshima (2022) Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Commun. Biol. 5, 707. doi: 10.1038/s42003-022-03668-3
Pub Med
Open Access
K. Kataoka, S. Suzuki, T. Tenno, N. Goda, E. Hibino, A. Oshima, H. Hiroaki (2022) A cryptic phosphate-binding pocket on the SPFH domain of human stomatin that regulates a novel fibril-like self-assembly. Curr. Res. Struct. Biol. 4:158-166. doi: 10.1016/j.crstbi.2022.05.002
Pub Med
Open Access
S. Tanaka, M. Morita, T. Yamagishi, H. Madapally, K. Hayashida, H. Khandelia, C. Gerle, H. Shigematsu, A. Oshima, K. Abe (2022) Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J. Med. Chem. 2022, 65, 11, 7843?7853. doi: 10.1021/acs.jmedchem.2c00338
Pub Med
Open Access
C. Akıl, S. Ali, L. T. Tran, J. Gaillard, W. Li, K. Hayashida, M. Hirose, T. Kato, A. Oshima, K. Fujishima, L. Blanchoin, A. Narita, R. C. Robinson (2022) Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Sci. Adv. 8(12), eabm2225. doi: 10.1126/sciadv.abm2225
Pub Med
Open Access
M. Kuzuya, H. Hirano, K. Hayashida, M. Watanabe, K. Kobayashi, T. Terada, M. I. Mahmood, F. Tama, K. Tani, Y. Fujiyoshi, A. Oshima (2022) Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N-terminus and phospholipids. Sci. Signal. 15, eabg6941. doi: 10.1126/scisignal.abg6941
Pub Med
Free Access
H. Nakanishi, K. Hayashida, T. Nishizawa, A. Oshima, K. Abe (2022) Cryo-EM of the ATP11C flippase reconstituted in Nanodiscs shows a distended phospholipid bilayer inner membrane around transmembrane helix 2. J. Biol. Chem. 298, 101498. doi: 10.1016/j.jbc.2021.101498
Pub Med
Open Access
2020
S. Endo, H. Oguri, J. Segawa, M. Kawai, D. Hu, S. Xia, T. Okada, K. Irie, S. Fujii, H. Gouda, K. Iguchi, T. Matsukawa, N. Fujimoto, T. Nakayama, N. Toyooka, T. Matsunaga, A. Ikari (2020) Development of Novel AKR1C3 Inhibitors as New Potential Treatment for Castration-Resistant Prostate Cancer. J Med Chem. 63:10396-10411. doi: 10.1021/acs.jmedchem.0c00939
Pub Med
Open Access
H. Nakanishi, T. Nishizawa, K. Segawa, O. Nureki, Y. Fujiyoshi, S. Nagata, K. Abe (2020) Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM. Cell Rep. 32:108208. doi: 10.1016/j.celrep.2020.108208.
Pub Med
K. Ikeda, S. Suzuki, Y. Shigemitsu, T. Tenno, N. Goda, A. Oshima, H. Hiroaki (2020) Presence of intrinsically disordered proteins can inhibit the nucleation phase of amyloid fibril formation of Aβ(1?42) in amino acid sequence independent manner. Sci Rep. 10:12334
Pub Med
Open Access
H. Nakanishi, K. Irie, K. Segawa, K. Hasegawa, Y. Fujiyoshi, S. Nagata, K. Abe (2020) Crystal structure of a human plasma membrane phospholipid flippase. J J. Biol. Chem. 295:10180-10194
Pub Med
Open Access
S. Miller, Y. Son, Y. Aikawa, E. Makino, Y. Nagai, A. Srivastava, T. Oshima, A. Sugiyama, A. Hara, K. Abe, K. Hirata, S. Oishi, S. Hagihara, A. Sato, F. Tama, K. Itami, S. Kay, M. Hatori, T. Hirota, (2020) Isoform-selective Regulation of Mammalian Cryptochromes. Nat Chem Biol. 16, 676?685
Pub Med
A. Oshima (2020) Structural insights into gap junction channels boosted by cryo-EM. Curr. Opin. Struct. Biol. 63, 42-48
Pub Med
T. Shimomura, Y. Yonekawa, H. Nagura, M. Tateyama, Y. Fujiyoshi, K. Irie (2020) A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence. eLife 9, e52828.
Open Access
Insight Article
Press Release
research highlights (Nature)
B. Burendei, R. Shinozaki, M. Watanabe, T. Terada, K. Tani, Y. Fujiyoshi, A. Oshima (2020) Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids. Sci. Adv. 6, eaax3157
Pub Med
Open Access
2019
A. Urbani, V. Giorgio, A. Carrer, C. Franchin, G. Arrigoni, C. Jiko, K. Abe, S. Maeda, K. Shinzawa-Itoh, J. F. M. Bogers, D. G. G. McMillan, C. Gerle, I. Szabo, P. Bernardi (2019) Purified F-ATP synthase forms a Ca2+-dependent high-conductance channel matching the mitochondrial permeability transition pore. Nat. Commun.10, 4341
Pub Med
K. Yamamoto, V. Dubey, K. Irie, H. Nakanishi, H. Khandelia, Y. Fujiyoshi, K. Abe (2019) A single K+-binding site in the crystal structure of the gastric proton pump. eLife 8, e47701.
Pub Med
Press Release
A. Kamiya, Y. Hayama, S. Kato, A. Shimomura, T. Shimomura, K. Irie, R. Kaneko, Y. Yanagawa, K. Kobayashi, T. Ochiya (2019) Genetic manipulation of autonomic nerve fiber innervation and activity and its effect on breast cancer progression. Nat. Neurosci. 22:1289-1305
Pub Med
A. Oshima (2019) Potential of cryo-EM for high-resolution structural analysis of gap junction channels. Curr. Opin. Struct. Biol. 54:78-85
Pub Med
S. Nakamura, K. Irie, H. Tanaka, K. Nishikawa, H. Suzuki, A. Tamura, S. Tsukita, Y. Fujiyoshi (2019) Morphologic determinant of tight junctions revealed by claudin-3 structures. Nat. Commun.10,816
Pub Med
2018
S. Nakamura, Y. Fujiyoshi, K. Irie (2018)Enhancement of the thermostability of mouse claudin-3 on complex formation with the carboxyl-terminal region of Clostridium perfringens enterotoxin improves crystal quality. Acta Crystallogr. F Struct. Biol. Commun. 74(Pt 3):150-155.
Pub Med
K. Abe, K. Irie, H. Nakanishi, H. Suzuki, Y. Fujiyoshi (2018) Crystal structures of the gastric proton pump. Nature 556:214-218
Pub Med
K. Irie, Y. Haga, T. Shimomura, Y. Fujiyoshi (2018) Optimized expression and purification of NavAb provide the structural insight into the voltage dependence. FEBS Lett. 592:274-283
Pub Med
2017
A. Oshima (2017) Structure of an innexin gap junction channel and cryo-EM sample preparation. Microscopy 66:371-379
Pub Med
Open Access
W. Shihoya, T. Nishizawa, K. Yamashita, A. Inoue, K. Hirata, F.M.N. Kadji, A. Okuta, K. Tani, J. Aoki, Y. Fujiyoshi, T. Doi, O. Nureki (2017) X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog. Nat. Struct. Mol. Biol. 24:758-764
Pub Med
K. Abe, J. Shimokawa, M. Naito, K. Munson, O. Vagin, G. Sachs, H. Suzuki, K. Tani, Y. Fujiyoshi (2017) The cryo-EM structure of gastric H+,K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitors. Sci. Rep. 7:6632
Pub Med
Open Access
H. Suzuki, K. Tani, Y. Fujiyoshi (2017) Crystal structures of claudins: insights into their intermolecular interactions. Ann. N. Y. Acad. Sci. 1397:25-34
Pub Med
Open Access
2016
A. Oshima, K. Tani, Y. Fujiyoshi (2016) Atomic structure of the innexin-6 gap junction channel determined by cryo-EM. Nat. Commun. 7:13681.
Pub Med
Open Access
W. Shihoya, T. Nishizawa, A. Okuta, K. Tani, N. Dohmae, Y. Fujiyoshi, O. Nureki, T. Doi (2016) Activation mechanism of endothelin ETB receptor by endothelin-1. Nature 537:363-368
Pub Med
T. Shimomura, K. Irie, Y. Fujiyoshi (2016) Molecular determinants of prokaryotic voltage-gated sodium channels for recognition of local anesthetics. FEBS J. 283:2881-2895.
Pub Med
K. Abe, Y. Fujiyoshi (2016) Cryo-electron microscopy for structure analyses of membrane proteins in the lipid bilayer. Curr. Opin. Struct. Biol. 39:71-78
Pub Med
A. Okuta, K. Tani, S. Nishimura, Y. Fujiyoshi, T. Doi (2016) Thermostabilization of the human endothelin type-B receptor. J. Mol. Biol. 428:2265-2274.
Pub Med
A. Oshima, T. Matsuzawa, K. Murata, K. Tani, Y. Fujiyoshi (2016) Hexadecameric structure of an invertebrate gap junction channel. J. Mol. Biol. 428:1227-1236.
Pub Med
Open Access
H. Tanaka, Y. Yamamoto, H. Kashihara, Y. Yamazaki, K. Tani, Y. Fujiyoshi, K. Mineta, K. Takeuchi, A. Tamura, S. Tsukita (2016) Claudin-21 has a paracellular channel role at tight junctions. Mol. Cell Biol. 36:954-964.
Pub Med
H. Nagura, T. Doi, Y. Fujiyoshi (2016) Characterization of physiologic phenotypes of dentate gyrus synapses of PDZ1/2 domain-deficient PSD-95 knockin mice. Eur. J. Neurosci. 43:618-625.
Pub Med
A. Kamegawa, Y. Hiroaki, K. Tani, Y. Fujiyoshi (2016) Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide. Microscopy (Oxf) 65:177-184.
Pub Med
Open Access
Y. Bando, K. Irie, T. Shimomura, H. Umeshima, Y. Kushida, M. Kengaku, Y. Fujiyoshi, T. Hirano, Y. Tagawa (2016) Control of Spontaneous Ca2+ Transients Is Critical for Neuronal Maturation in the Developing Neocortex. Cereb. Cortex. 26:106-117.
Pub Med
2015
Y. Fujiyoshi (2015) Development of the field of structural physiology. Proc. Jpn. Acad. Ser. B. Phys. Biol. Sci. 91:447-468.
Pub Med
Open Access
F. Hauer, C. Gerle, N. Fischer, A. Oshima, K. Shinzawa Itoh, S. Shimada, K. Yokoyama, Y. Fujiyoshi, H. Stark (2015) GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM. Structure 23:1769-1775
Pub Med
K. Minatohara, Y. Murata, Y. Fujiyoshi, T. Doi (2015) An Intracellular Domain with a Novel Sequence Regulates Cell Surface Expression and Synaptic Clustering of Leucine-Rich Repeat Transmembrane Proteins in Hippocampal Neurons. J Neurochem. 134:618-628
Pub Med
C. Jiko, K.M. Davies, K. Shinzawa-Itoh, K. Tani, S. Maeda, D.J. Mills, T. Tsukihara, Y. Fujiyoshi, W. Kuhlbrandt, C. Gerle (2015) Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals. Elife. 4:e06119
Pub Med
Open Access
Y. Saitoh, H. Suzuki, K. Tani, K. Nishikawa, K. Irie, Y. Ogura, A. Tamura, S. Tsukita, Y. Fujiyoshi (2015) Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin. Science 347:775-778
Free AccessPub Med
H. Suzuki, K. Tani, A. Tamura, S. Tsukita, Y. Fujiyoshi (2015) Model for the architecture of claudin-based paracellular ion channels through tight junctions. J. Mol. Biol. 427:291-297
Pub Med
Open Access
2014
K. Abe, K. Tani, Y. Fujiyoshi (2014) Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating. J. Biol. Chem. 289:40590-30601
Pub Med
Open Access
H. Suzuki, T. Nishizawa, K. Tani, Y. Yamazaki, A. Tamura, R. Ishitani, N. Dohmae, S. Tsukita, O. Nureki, Y. Fujiyoshi (2014) Crystal Structure of a Claudin Provides Insight into the Architecture of Tight Junctions. Science 344:304-307
Free AccessPub Med
D. Morito, K. Nishikawa, J. Hoseki, A. Kitamura, Y. Kotani, K. Kiso, M. Kinjo, Y. Fujiyoshi, K. Nagata (2014) Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state. Sci. Rep. 4:4442
Pub Med
Open Access
K. Tani, Y. Fujiyoshi (2014) Water channel structures analysed by electron crystallography. Biochim. Biophys. Acta. 1840:1605-1613
Pub Med
2013
F. Yang, K. Abe, K. Tani, Y. Fujiyoshi (2013) Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy. Microscopy (Oxf) 62:597-606
Pub Med
Open Access
C.J. Tsai, K. Tani, K. Irie, Y. Hiroaki, T. Shimomura, D.G. McMillan, G.M. Cook, G.F.X. Schertler, Y. Fujiyoshi, X.D. Li (2013) Two alternative conformations of a voltage-gated sodium channel. J. Mol. Biol. 425:4074-4088.
Pub Med
Open Access
H. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. Tsukita (2013) The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat. Nat. Commun. 4:1766.
Pub Med
Open Access
K. Tani, C. P. Arthur, M. Tamakoshi, K. Yokoyama, K. Mitsuoka, Y. Fujiyoshi, C. Gerle (2013) Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus thermophilus. Microscopy (Oxf) 62:467-474
Pub Med
Open Access
M. Goda, Y. Fujiyoshi, M. Sugimoto, R. Fujii (2013) Novel Dichromatic Chromatophores in the Integument of the Mandarin Fish Synchiropus splendidus. Biol. Bull. 224:14-17.
Pub Med
Open Access
A. Oshima, T. Matsuzawa, K. Nishikawa, Y. Fujiyoshi (2013) Oligomeric structure and functional characterization of C. elegans innexin-6 gap junction channels. J. Biol. Chem. 288:10513-10521.
Pub Med
Open Access
K. Minatohara, S. H. Ichikawa, T. Seki, Y. Fujiyoshi, T. Doi (2013) Ligand binding of PDZ domains has various roles in the synaptic clustering of SAP102 and PSD-95. Neurosci. Lett. 533:44-49.
Pub Med
2012
H. Nagura, Y. Ishikawa, K. Kobayashi, K. Takao, T. Tanaka, K. Nishikawa, H. Tamura, S. Shiosaka, H. Suzuki, T. Miyakawa, Y. Fujiyoshi, T. Doi (2012) Impaired synaptic clustering of postsynaptic density proteins and altered signal transmission in hippocampal neurons, and disrupted learning behavior in PDZ1 and PDZ2 ligand binding-deficient PSD-95 knockin mice. Mol Brain 5:43.
Pub Med
Open Access
K. Abe, K. Tani, T. Friedrich, Y. Fujiyoshi (2012) Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site. Proc. Natl. Acad. Sci. U.S.A. 109:18401-18406
Pub Med
Open Access
N. Unwin, Y. Fujiyoshi (2012) Gating movement of acetylcholine receptor caught by plunge-freezing. J. Mol. Biol. 422:617-634.
Pub Med
Open Access
K. Irie, T. Shimomura, Y. Fujiyoshi (2012) The C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate. Nat. Commun. 3:793.
Pub Med
Open Access