参考文献｜クライオ電子顕微鏡支援

参考文献

研究

Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes

K. Tani, Kazumi Kobayashi, Naoki Hosogi, Xuan-Cheng Ji, Sakiko Nagashima, Kenji V. P. Nagashima, Airi Izumida, Kazuhito Inoue, Yusuke Tsukatani, Ryo Kanno, Malgorzata Hall, Long-Jiang Yu, Isamu Ishikawa, Yoshihiro Okura, Michael T Madigan, Akira Mizoguchi, Bruno M Humbel, Yukihiro Kimura, Zheng-Yu Wang-Otomo J. Biol. Chem. (2022) 298:101967 (Open Access)

研究成果は三重大学でも紹介されています。
Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

K. Tani, Ryo Kanno, Riku Kikuchi, Saki Kawamura, Kenji V. P. Nagashima, Malgorzata Hall, Ai Takahashi, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Z.-Y. Wang-Otomo nat. communs. (2022) 13:1904 (Open Access)

研究成果は三重大学でも紹介されています。
Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.

M. Kuzuya, H. Hirano, K. Hayashida, M. Watanabe, K. Kobayashi, T. Terada, M.I. Mahmood, F. Tama, K. Tani, Y. Fujiyoshi, A. Oshima Sci Signal (2022) 15:eabg6941
研究成果は名古屋大学にて紹介されています。
Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

K. Tani, Ryo Kanno, Riku Kikuchi, Saki Kawamura, Kenji V. P. Nagashima, Malgorzata Hall, Ai Takahashi, Long-Jiang Yu, Yukihiro Kimura, Michael T. Madigan, Akira Mizoguchi, Bruno M. Humbel, Z.-Y. Wang-Otomo bioRxiv (2021) (On-line)
A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

K. Tani, K. V. P. Nagashima, R. Kanno, S. Kawamura, R. Kikuchi, M. Hall, L.-J. Yu, Y. Kimura, M. T. Madigan, A. Mizoguchi, B. M. Humbel, Z.-Y. Wang-Otomo nat. communs. (2021) 12:6300 (Open Access)

研究成果は三重大学、AMED、日経バイオテク、Editors’ Highlights webpageでも紹介されています。
Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.

K. Tani, R. Kanno, X.-C. Ji, M. Hall, L.-J. Yu, Y. Kimura, M. T. Madigan, A. Mizoguchi, B. M. Humbel, Z.-Y. Wang-Otomo biochemistry (2021) 62: 2483-2491

研究成果は三重大学、AMEDでも紹介されています。
A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

K. Tani, K. V. P. Nagashima, R. Kanno, S. Kawamura, R. Kikuchi, M. Hall, L.-J. Yu, Y. Kimura, M. T. Madigan, A. Mizoguchi, B. M. Humbel, Z.-Y. Wang-Otomo bioRxiv (2021) (On-line)
Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.

K. Tani, R. Kanno, X.-C. Ji, M. Hall, L.-J. Yu, Y. Kimura, M. T. Madigan, A. Mizoguchi, B. M. Humbel, Z.-Y. Wang-Otomo bioRxiv (2021) (On-line)
Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.

K. Hiragi, K. Nishio, S. Moriyama, T. Hamaguchi, A. Mizoguchi, K. Yonekura, K. Tani, T. Mizushima J. Struct. Biol. (2021) 213:107748
Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.

K. Tani, R. Kanno, Y. Makino, M. Hall, M. Takenouchi, M. Imanishi, L.-J. Yu, J. Overmann, M. T. Madigan, Y. Kimura, A. Mizoguchi, B. M. Humbel , Z.-Y. Wang-Otomo nat. communs. (2020) 11:4955(Open Access)
Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal.

T. Doi, K. Kikuta, K. Tani Biochemistry (2020) 59:1718-1727
Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy grid.

Y. Yokoyama, T. Terada, K. Shimizu, K. Nishikawa, D. Kozai, A. Shimada, A. Mizoguchi, Y. Fujiyoshi, K. Tani Biophys. Rev. (2020) 12:349-354.
Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids.

B. Burendei, R. Shinozaki, M. Watanabe, T. Terada, K. Tani, Y. Fujiyoshi, A. Oshima Sci. Adv. (2020) 6:eaax3157.(Open Access)
Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy.

H. Yamaguchi, A. Kamegawa, K. Nakata, T. Kashiwagi, T. Mizukoshi*, Y. Fujiyoshi*, K. Tani*, J. Struct. Biol. (2019) 205:11-21.(Open Access)
X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog.

S. 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, Nat. Struct. Mol. Biol. (2017) 24:758-764.
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.

K. Abe, J. Shimokawa, M. Naito, K. Munson, O. Vagin, G. Sachs, H. Suzuki, K. Tani, Y. Fujiyoshi, Sci. Rep. (2017) 7:6632.
Atomic structure of the innexin-6 gap junction channel determined by cryo-EM.

A. Oshima, K. Tani, Y. Fujiyoshi, Nat. commun. (2016) 7: 13681.
Activation mechanism of endothelin ETB receptor by endothelin-1.

W. Shihoya, T. Nishizawa, A. Okuta, K. Tani, N. Dohmae, Y. Fujiyoshi, O. Nureki, T. Doi, Nature (2016) 537:363-368.
Thermostabilization of the human endothelin type-B receptor.

A. Okuta, K. Tani, S. Nishimura, Y. Fujiyoshi, T. Doi, J. Mol. Biol. (2016) 428:2265-2274.
Hexadecameric structure of an invertebrate gap junction channel.

A. Oshima, T. Matsuzawa, K. Murata, K. Tani, Y. Fujiyoshi, J. Mol. Biol. (2016) 428:1227-1236.
Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.

Y. Osuda, K. Shinzawa-Itoh, K. Tani, S. Yoshikawa, T. Tsukihara, C. Gerle, Microscopy (2016) 65:263-267.
Claudin-21 has a paracellular channel role at tight junctions.

H. Tanaka, Y. Yamamoto, H. Kashihara, Y. Yamazaki, K. Tani, Y. Fujiyoshi, K. Mineta, K. Takeuchi, A. Tamura, S. Tsukita, Mol. Cell Biol. (2016) 36:954-964.
Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide.

A. Kamegawa, Y. Hiroaki, K. Tani$, Y. Fujiyoshi$,, Microscopy 65:177-184.
Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals.

C. Jiko, K.M. Davies, K. Shinzawa-Itoh, K. Tani, S. Maeda, D.J. Mills, T. Tsukihara, Y. Fujiyoshi, W. Kuhlbrandt, C. Gerle, eLife (2015) 4:e06119.
Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin.

Y. Saitoh*, H. Suzuki*, K. Tani*, K. Nishikawa, K. Irie, Y. Ogura, A. Tamura, S. Tsukita, Y. Fujiyoshi, Science (2015) 347:775-778.
Model for the architecture of claudin-based paracellular ion channels through tight junctions.

H. Suzuki*, K. Tani*, A. Tamura, S. Tsukita, Y. Fujiyoshi, J. Mol. Biol. (2015) 427:291-297.
Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating.

K. Abe, K. Tani, Y. Fujiyoshi, J. Biol. Chem. (2014) 289:30590-30601.
Crystal structure of a claudin provides insight into the architecture of tight junctions.

H. Suzuki*, T. Nishizawa*, K. Tani*, Y. Yamazaki, A. Tamura, R. Ishitani, N. Dohmae, S. Tsukita, O. Nureki, Y. Fujiyoshi, Science (2014) 344:304-307.
Three-dimensional structure of bovine heart NADH:ubiquinone oxidoreductase (complex I) by electron microscopy of a single negatively stained two-dimensional crystal.

S. Shimada, K. S-Itoh, S. Amano, Y. Akira, A. Miyazawa, T. Tsukihara, K. Tani, C. Gerle, S. Yoshikawa, Microscopy (2014) 63:167-174.
Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondria.

S. Maeda, K. S-Itoh, K. Mieda, M. Yamamoto, Y. Nakashima, Y. Ogasawara, C. Jiko, K. Tani, A. Miyazawa, C. Gerle, S. Yoshikawa, Acta Cryst. (2013) F69:1368-1370.
Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy.

F. Yang, K. Abe, K. Tani, Y. Fujiyoshi, Microscopy (2013) 62:597-606.
Two alternative conformations of a voltage-gated sodium channel.

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, J. Mol. Biol. (2013) 425:4074-4088.
Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus Thermophilus.

K. Tani, C.P. Arthur, M. Tamakoshi, K. Yokoyama, K. Mitsuoka, Y. Fujiyoshi, C. Gerle, Microscopy (2013) 62:467-474.
Strand formation by a trimeric unit repeat of four-transmembrane proteins in Euglena.

H. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. Tsukita, Nat. commun. (2013) 4:1766.
Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site.

K. Abe, K. Tani, T. Friedrich, Y. Fujiyoshi, Proc. Natl. Acad. Sci. U. S. A. (2012) 109:18401-18406.
Conformational rearrangement of gastric H+,K+-ATPase induced by an acid suppressant.

K. Abe, K. Tani, Y. Fujiyoshi, Nat. commun. (2011) 2:155.
Asymmetric Configurations and N-terminal Rearrangements in Connexin26 Gap Junction Channels.

A. Oshima, K. Tani, M. M. Toloue, Y. Hiroaki, A. Smock, S. Inukai, A. Cone, B. J. Nicholson, G. E. Sosinsky, Y. Fujiyoshi, J. Mol. Biol. (2011) 405:724-735.
Water permeability and characterization of aquaporin-11

K. Yakata, K. Tani$, Y. Fujiyoshi, J. Struct. Biol. (2011) 174:315-320.
Influence of the cytoplasmic domains of aquaporin-4 on water conduction and array formation

T. Mitsuma*, K. Tani*, Y. Hiroaki, A. Kamegawa, H. Suzuki, H. Hibino, Y. Kurachi, Y. Fujiyoshi, J. Mol. Biol. (2010) 402:669-681.
Structural and functional characterization of H+, K+-ATPase with bound fluorinated phosphate analogs.

K. Abe, K. Tani, Y. Fujiyoshi, J. Struct. Biol. (2010) 170:60-68.
Mechanism of aquaporin-4's fast and highly selective water conductance and proton exclusion.

K. Tani*, T. Mitsuma*, Y. Hiroaki, A. Kamegawa, K. Nishikawa, Y. Tanimura, Y. Fujiyoshi, J. Mol. Biol. (2009) 389:694-706.
Inter-Subunit Interaction of Gastric H+,K+-ATPase Prevents Reverse Reaction of the Transport Cycle.

K. Abe, K. Tani, T. Nishizawa, Y. Fujiyoshi, EMBO J. (2009) 28:1637-1643.
Projection structure of a N-terminal deletion mutant of connexin 26 channel with decreased central pore density.

A. Oshima, K. Tani, Y. Hiroaki, Y. Fujiyoshi, G. E. Sosinsky, Cell. Commun. Adhes. (2008) 15:85-93.
Structural analysis of 2D crystals of gastric H+,K+-ATPase in different states of the transport Cycle.

T. Nishizawa, K. Abe, K. Tani, Y. Fujiyoshi, J. Struct. Bol. (2008) 162:219-228.
Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophiles.

M. Toei, C. Gerle, M. Nakano, K. Tani, N. Gyobu, M. Tamakoshi, N. Sone, M. Yoshida, Y. Fujiyoshi, K. Mitsuoka, K. Yokoyama, Proc. Natl. Acad. Sci. U. S. A. (2007) 104:20256-20261.
Three-dimensional structure of a human connexin26 gap junction channel reveals a plug in the Vestibule.

A. Oshima, K. Tani, Y. Hiroaki, Y. Fujiyoshi, G. E. Sosinsky, Proc. Natl. Acad. Sci. U. S. A. (2007) 104:10034-10039.
Implications of the Aquaporin-4 Structure on Array Formation and Cell Adhesion.

Y. Hiroaki*, K. Tani*, A. Kamegawa, N. Gyobu, K. Nishikawa, H. Suzuki, T. Walz, S. Sasaki, K. Mitsuoka, K. Kimura, A. Mizoguchi, Y. Fujiyoshi, J. Mol. Biol. (2006) 355:628-639.
Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilius V-ATPase.

C. Gerle, K. Tani, K. Yokoyama, M. Tamakoshi, M. Yoshida, Y. Fujiyoshi, K. Mitsuoka, J. Struct. Biol. (2006) 153:200-206.
Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).

T. Maeda, M. Inoue, S. Koshiba, T. Yabuki, M. Aoki, E. Nunokawa, E. Seki, T. Matsuda, Y. Motoda, A. Kobayashi, F. Hiroyasu, M. Shirouzu, T. Terada, N. Hayami, Y. Ishizuka, N. Shinya, A. Tatsuguchi, M. Yoshida, H. Hirota, Y. Matsuo, K. Tani, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, S. Yokoyama, J. Biol. Chem. (2004) 279:13174-13182.
Solution structure of a BolA-like protein from Mus musculus.

T. Kasai, M. Inoue, S. Koshiba, T. Yabuki, M. Aoki, E. Nunokawa, E. Seki, T. Matsuda, N. Matsuda, Y. Tomo, M. Shirouzu, T. Terada, N. Obayashi, H. Hamana, N. Shinya, A. Tatsuguchi, S. Yasuda, M. Yoshida, H. Hirota, Y. Matsuo, K. Tani, H. Suzuki, T. Arakawa, P. Carninci, J. Kawai, Y. Hayashizaki, T. Kigawa, S. Yokoyama, Protein Sci. (2004) 13:545-548.
Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique.

N. Gyobu, K. Tani, Y. Hiroaki, A. Kamegawa, K. Mitsuoka, Y. Fujiyoshi, J. Struct. Biol. (2004) 146: 325-333.
Inositol 1,4,5-trisphosphate Receptor Contains Multiple Cavities and L-shaped Ligand-binding Domains.

C. Sato, K. Hamada, T. Ogura, A. Miyazawa, K. Iwasaki, Y. Hiroaki, K. Tani, A. Terauchi, Y. Fujiyoshi, K. Mikoshiba, J. Mol. Biol. (2004) 336:155-164.
Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics.

Y. Kuroda, K. Tani, Y. Matsuo, S. Yokoyama, Protein Sci. (2000) 9:2313-2321.
A set of computer programs for determining defocus and astigmatism in electron images.

K. Tani, H. Sasabe and C. Toyoshima, Ultramicroscopy (1996) 65:31-44.

クライオ電子顕微鏡 技術・教育支援

参考文献

研究

Ca2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes

Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.

Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.

A Novel Membrane Protein in the Rhodobacter sphaeroides LH1-RC Photocomplex

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum.

Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.

Cryo-EM structure of a Ca2+-bound photosynthetic LH1-RC complex containing multiple αβ-polypeptides.

Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal.

Development of a deep learning-based method to identify “good” regions of a cryo-electron microscopy grid.

Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids.

Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy.

X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog.

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.

Atomic structure of the innexin-6 gap junction channel determined by cryo-EM.

Activation mechanism of endothelin ETB receptor by endothelin-1.

Thermostabilization of the human endothelin type-B receptor.

Hexadecameric structure of an invertebrate gap junction channel.

Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.

Claudin-21 has a paracellular channel role at tight junctions.

Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide.

Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals.

Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin.

Model for the architecture of claudin-based paracellular ion channels through tight junctions.

Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating.

Crystal structure of a claudin provides insight into the architecture of tight junctions.

Three-dimensional structure of bovine heart NADH:ubiquinone oxidoreductase (complex I) by electron microscopy of a single negatively stained two-dimensional crystal.

Two-dimensional crystallization of intact F-ATP synthase isolated from bovine heart mitochondria.

Carbon sandwich preparation preserves quality of two-dimensional crystals for cryo-electron microscopy.

Two alternative conformations of a voltage-gated sodium channel.

Visualization of two distinct states of disassembly in the bacterial V-ATPase from Thermus Thermophilus.

Strand formation by a trimeric unit repeat of four-transmembrane proteins in Euglena.

Cryo-EM structure of gastric H+,K+-ATPase with a single occupied cation-binding site.

Conformational rearrangement of gastric H+,K+-ATPase induced by an acid suppressant.

Asymmetric Configurations and N-terminal Rearrangements in Connexin26 Gap Junction Channels.

Water permeability and characterization of aquaporin-11

Influence of the cytoplasmic domains of aquaporin-4 on water conduction and array formation

Structural and functional characterization of H+, K+-ATPase with bound fluorinated phosphate analogs.

Mechanism of aquaporin-4's fast and highly selective water conductance and proton exclusion.

Inter-Subunit Interaction of Gastric H+,K+-ATPase Prevents Reverse Reaction of the Transport Cycle.

Projection structure of a N-terminal deletion mutant of connexin 26 channel with decreased central pore density.

Structural analysis of 2D crystals of gastric H+,K+-ATPase in different states of the transport Cycle.

Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophiles.

Three-dimensional structure of a human connexin26 gap junction channel reveals a plug in the Vestibule.

Implications of the Aquaporin-4 Structure on Array Formation and Cell Adhesion.

Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilius V-ATPase.

Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16).

Solution structure of a BolA-like protein from Mus musculus.

Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique.

Inositol 1,4,5-trisphosphate Receptor Contains Multiple Cavities and L-shaped Ligand-binding Domains.

Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics.

A set of computer programs for determining defocus and astigmatism in electron images.

レビュー($: corresponding author)

Leucine Dehydrogenase: Structure and Thermostability.

Crystal structures of claudins: insights into their intermolecular interactions.

Water channel structures analysed by electron crystallography.

クライオ電子顕微鏡　技術・教育支援