8BW7
 
 | | Cryo-EM structure of rat SLC22A6 bound to alpha-ketoglutaric acid | | Descriptor: | 2-OXOGLUTARIC ACID, CHLORIDE ION, Solute carrier family 22 member 6, ... | | Authors: | Parker, J.L, Kato, T, Newstead, S. | | Deposit date: | 2022-12-06 | | Release date: | 2023-07-19 | | Last modified: | 2023-11-22 | | Method: | ELECTRON MICROSCOPY (3.53 Å) | | Cite: | Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1.
Nat.Struct.Mol.Biol., 30, 2023
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8BVR
 | | Cryo-EM structure of rat SLC22A6 in the apo state | | Descriptor: | PHOSPHATE ION, Solute carrier family 22 member 6, Synthetic nanobody (Sybody) | | Authors: | Parker, J.L, Kato, T, Newstead, S. | | Deposit date: | 2022-12-05 | | Release date: | 2023-07-19 | | Last modified: | 2023-11-22 | | Method: | ELECTRON MICROSCOPY (3.52 Å) | | Cite: | Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1.
Nat.Struct.Mol.Biol., 30, 2023
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8HLB
 | | Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 | | Descriptor: | TR109 heavy chain, TR109 light chain, TR92 heavy chain, ... | | Authors: | Akiba, H, Fujita, J, Ise, T, Nishiyama, K, Miyata, T, Kato, T, Namba, K, Ohno, H, Kamada, H, Nagata, S, Tsumoto, K. | | Deposit date: | 2022-11-29 | | Release date: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (3.63 Å) | | Cite: | Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.
Commun Biol, 6, 2023
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8GQY
 | | CryoEM structure of pentameric MotA from Aquifex aeolicus | | Descriptor: | Motility protein A | | Authors: | Nishikino, T, Takekawa, N, Kishikawa, J, Hirose, M, Onoe, S, Kato, T, Imada, K. | | Deposit date: | 2022-08-31 | | Release date: | 2022-10-26 | | Last modified: | 2022-11-09 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structure of MotA, a flagellar stator protein, from hyperthermophile.
Biochem.Biophys.Res.Commun., 631, 2022
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8HIQ
 | | cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP | | Descriptor: | Glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Wakabayashi, T, Oide, M, Kato, T, Nakasako, M. | | Deposit date: | 2022-11-21 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-20 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Febs J., 290, 2023
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8HJ3
 | | cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP | | Descriptor: | Glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Wakabayashi, T, Oide, M, Kato, T, Nakasako, M. | | Deposit date: | 2022-11-22 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-20 | | Method: | ELECTRON MICROSCOPY (3.29 Å) | | Cite: | Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Febs J., 290, 2023
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8HHO
 | | cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP | | Descriptor: | Glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Wakabayashi, T, Oide, M, Kato, T, Nakasako, M. | | Deposit date: | 2022-11-16 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-20 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Febs J., 290, 2023
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8HJ9
 | | cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP | | Descriptor: | Glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Wakabayashi, T, Oide, M, Kato, T, Nakasako, M. | | Deposit date: | 2022-11-22 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-20 | | Method: | ELECTRON MICROSCOPY (3.12 Å) | | Cite: | Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Febs J., 290, 2023
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8HIZ
 | | cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP | | Descriptor: | Glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Wakabayashi, T, Oide, M, Kato, T, Nakasako, M. | | Deposit date: | 2022-11-22 | | Release date: | 2023-02-08 | | Last modified: | 2023-12-20 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
Febs J., 290, 2023
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8OMU
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8P6A
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6JY0
 | | CryoEM structure of S.typhimurium R-type straight flagellar filament made of FljB (A461V) | | Descriptor: | Flagellin | | Authors: | Yamaguchi, T, Toma, S, Terahara, N, Miyata, T, Minamino, T, Ashikara, M, Namba, K, Kato, T. | | Deposit date: | 2019-04-25 | | Release date: | 2020-02-19 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.56 Å) | | Cite: | Structural and Functional Comparison ofSalmonellaFlagellar Filaments Composed of FljB and FliC.
Biomolecules, 10, 2020
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7C86
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-05-28 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7E6X
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-02-24 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7E71
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-02-24 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7E6Z
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-02-24 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7E70
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-02-24 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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7E6Y
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-02-24 | | Release date: | 2021-04-07 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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6O97
 | | Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution | | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxyc yclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside, 16S Ribosomal RNA, 23S Ribosomal RNA, ... | | Authors: | Matsushita, T, Sati, G.C, Kondasinghe, N, Pirrone, M.G, Kato, T, Waduge, P, Kumar, H.S, Sanchon, A.C, Dobosz-Bartoszek, M, Shcherbakov, D, Juhas, M, Hobbie, S.N, Schrepfer, T, Chow, C.S, Polikanov, Y.S, Schacht, J, Vasella, A, Bottger, E.C, Crich, D. | | Deposit date: | 2019-03-13 | | Release date: | 2019-04-17 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc., 141, 2019
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7VNJ
 | | Complex structure of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) pore with short stem | | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosyltransferase enzymatic component, CALCIUM ION | | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | | Deposit date: | 2021-10-11 | | Release date: | 2022-10-26 | | Method: | ELECTRON MICROSCOPY (2.56 Å) | | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile.
Nat Commun, 13, 2022
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7VNN
 | | Complex structure of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) pore with long stem | | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, CALCIUM ION, CdtA | | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | | Deposit date: | 2021-10-11 | | Release date: | 2022-10-26 | | Last modified: | 2022-11-02 | | Method: | ELECTRON MICROSCOPY (2.64 Å) | | Cite: | Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile.
Nat Commun, 13, 2022
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7CLR
 | | CryoEM structure of S.typhimurium flagellar LP ring | | Descriptor: | Flagellar L-ring protein, Flagellar P-ring protein | | Authors: | Yamaguchi, T, Makino, F, Miyata, T, Minamino, T, Kato, T, Namba, K. | | Deposit date: | 2020-07-21 | | Release date: | 2021-06-02 | | Last modified: | 2021-12-22 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Structure of the molecular bushing of the bacterial flagellar motor.
Nat Commun, 12, 2021
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7DZY
 | | Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490 | | Descriptor: | Fab Heavy chain of enhancing antibody 2490, Fab light chain of enhancing antibody 2490, Spike glycoprotein | | Authors: | Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H. | | Deposit date: | 2021-01-26 | | Release date: | 2021-06-02 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.
Cell, 184, 2021
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7DZX
 | | Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2 | | Descriptor: | Fab Heavy chain of enhancing antibody, Fab light chain of enhancing antibody, Spike glycoprotein | | Authors: | Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H. | | Deposit date: | 2021-01-26 | | Release date: | 2021-06-02 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.53 Å) | | Cite: | An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.
Cell, 184, 2021
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7DZW
 | | Apo spike protein from SARS-CoV2 | | Descriptor: | Spike glycoprotein | | Authors: | Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H. | | Deposit date: | 2021-01-26 | | Release date: | 2021-06-02 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.45 Å) | | Cite: | An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.
Cell, 184, 2021
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