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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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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1IS1
| Crystal structure of ribosome recycling factor from Vibrio parahaemolyticus | Descriptor: | RIBOSOME RECYCLING FACTOR | Authors: | Nakano, H, Yamaichi, Y, Uchiyama, S, Yoshida, T, Nishina, K, Kato, H, Ohkubo, T, Honda, T, Yamagata, Y, Kobayashi, Y. | Deposit date: | 2001-11-05 | Release date: | 2003-06-17 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium J.BIOL.CHEM., 278, 2003
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7YVQ
| Complex structure of Clostridioides difficile binary toxin folded CDTa-bound CDTb-pore (short). | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosylating binary toxin enzymatic subunit CdtA, CALCIUM ION | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2022-08-19 | Release date: | 2022-10-26 | Last modified: | 2022-11-02 | Method: | ELECTRON MICROSCOPY (3.18 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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7YVS
| Complex structure of Clostridioides difficile binary toxin unfolded CDTa-bound CDTb-pore (short). | Descriptor: | ADP-ribosylating binary toxin binding subunit CdtB, ADP-ribosylating binary toxin enzymatic subunit CdtA, CALCIUM ION | Authors: | Yamada, T, Kawamoto, A, Yoshida, T, Sato, Y, Kato, T, Tsuge, H. | Deposit date: | 2022-08-19 | Release date: | 2022-10-26 | Last modified: | 2022-11-02 | Method: | ELECTRON MICROSCOPY (2.8 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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7CK5
| Solution structure of 28 amino acid polypeptide (354-381) in Plantago asiatica mosaic virus replicase bound to SDS micelle | Descriptor: | PlAMV replicase peptide from RNA-dependent RNA polymerase | Authors: | Komatsu, K, Sasaki, N, Yoshida, T, Suzuki, K, Masujima, Y, Hashimoto, M, Watanabe, S, Tochio, N, Kigawa, T, Yamaji, Y, Oshima, K, Namba, S, Nelson, R, Arie, T. | Deposit date: | 2020-07-15 | Release date: | 2021-07-21 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | Identification of a Proline-Kinked Amphipathic alpha-Helix Downstream from the Methyltransferase Domain of a Potexvirus Replicase and Its Role in Virus Replication and Perinuclear Complex Formation. J.Virol., 95, 2021
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1IY6
| Solution structure of OMSVP3 variant, P14C/N39C | Descriptor: | OMSVP3 | Authors: | Hemmi, H, Kumazaki, T, Yamazaki, T, Kojima, S, Yoshida, T, Kyogoku, Y, Katsu, M, Yokosawa, H, Miura, K, Kobayashi, Y. | Deposit date: | 2002-07-23 | Release date: | 2003-03-11 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond BIOCHEMISTRY, 42, 2003
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1IY5
| Solution structure of wild type OMSVP3 | Descriptor: | OMSVP3 | Authors: | Hemmi, H, Kumazaki, T, Yamazaki, T, Kojima, S, Yoshida, T, Kyogoku, Y, Katsu, M, Yokosawa, H, Miura, K, Kobayashi, Y. | Deposit date: | 2002-07-23 | Release date: | 2003-03-11 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond BIOCHEMISTRY, 42, 2003
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6LOS
| Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide. | Descriptor: | Collagen model peptide, type I, alpha 1, ... | Authors: | Kawahara, K, Maruno, T, Oki, H, Yoshida, T, Ohkubo, T, Koide, T, Kobayashi, Y. | Deposit date: | 2020-01-07 | Release date: | 2020-09-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.476 Å) | Cite: | Spatiotemporal regulation of PEDF signaling by type I collagen remodeling. Proc.Natl.Acad.Sci.USA, 117, 2020
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3B2C
| Crystal structure of the collagen triple helix model [{PRO-HYP(R)-GLY}4-{HYP(S)-Pro-GLY}2-{PRO-HYP(R)-GLY}4]3 | Descriptor: | Collagen-like peptide | Authors: | Motooka, D, Kawahara, K, Nakamura, S, Doi, M, Nishi, Y, Nishiuchi, Y, Nakazawa, T, Yoshida, T, Ohkubo, T, Kobayashi, Y, Kang, Y.K, Uchiyama, S. | Deposit date: | 2011-07-26 | Release date: | 2012-04-04 | Method: | X-RAY DIFFRACTION (1.36 Å) | Cite: | The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-pro-gly units Biopolymers, 98, 2011
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1ISE
| Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly | Descriptor: | Ribosome Recycling Factor | Authors: | Nakano, H, Yoshida, T, Oka, S, Uchiyama, S, Nishina, K, Ohkubo, T, Kato, H, Yamagata, Y, Kobayashi, Y. | Deposit date: | 2001-11-30 | Release date: | 2003-10-07 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly To be Published
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1IW4
| Solution structure of ascidian trypsin inhibitor | Descriptor: | trypsin inhibitor | Authors: | Hemmi, H, Yoshida, T, Kumazaki, T, Nemoto, N, Hasegawa, J, Nishioka, F, Kyogoku, Y, Yokosawa, H, Kobayashi, Y. | Deposit date: | 2002-04-19 | Release date: | 2002-08-28 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy. Biochemistry, 41, 2002
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3WCU
| The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Deoxygenated form | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | Deposit date: | 2013-06-01 | Release date: | 2014-06-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins Acta Crystallogr.,Sect.D, 70, 2014
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3WCV
| The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: CA bound form | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | Deposit date: | 2013-06-01 | Release date: | 2014-06-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins Acta Crystallogr.,Sect.D, 70, 2014
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3WCW
| The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: MG bound form | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | Deposit date: | 2013-06-01 | Release date: | 2014-06-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins Acta Crystallogr.,Sect.D, 70, 2014
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3WCT
| The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | Deposit date: | 2013-06-01 | Release date: | 2014-06-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins Acta Crystallogr.,Sect.D, 70, 2014
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3WJ4
| Crystal structure of PPARgamma ligand binding domain in complex with tributyltin | Descriptor: | Peroxisome proliferator-activated receptor gamma, tributylstannanyl | Authors: | Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T. | Deposit date: | 2013-10-04 | Release date: | 2014-10-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds To be Published
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3WJ5
| Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin | Descriptor: | Peroxisome proliferator-activated receptor gamma, triphenylstannanyl | Authors: | Harada, S, Hiromori, Y, Fukakusa, S, Kawahara, K, Nakamura, S, Noda, M, Uchiyama, S, Fukui, K, Nishikawa, J, Nagase, H, Kobayashi, Y, Ohkubo, T, Yoshida, T, Nakanishi, T. | Deposit date: | 2013-10-04 | Release date: | 2014-10-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds To be Published
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3WI0
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3WI1
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1VCK
| Crystal structure of ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10 | Descriptor: | FE (III) ION, FE2/S2 (INORGANIC) CLUSTER, HYDROSULFURIC ACID, ... | Authors: | Nam, J.-W, Noguchi, H, Fujiomoto, Z, Mizuno, H, Fushinobu, S, Kobashi, N, Iwata, K, Yoshida, T, Habe, H, Yamane, H, Omori, T, Nojiri, H. | Deposit date: | 2004-03-09 | Release date: | 2005-03-01 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system PROTEINS, 58, 2005
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1WW9
| Crystal structure of the terminal oxygenase component of carbazole 1,9a-dioxygenase, a non-heme iron oxygenase system catalyzing the novel angular dioxygenation for carbazole and dioxin | Descriptor: | FE (II) ION, FE2/S2 (INORGANIC) CLUSTER, terminal oxygenase component of carbazole | Authors: | Nojiri, H, Ashikawa, Y, Noguchi, H, Nam, J.-W, Urata, M, Fujimoto, Z, Mizuno, H, Yoshida, T, Habe, H, Omori, T. | Deposit date: | 2005-01-05 | Release date: | 2005-08-23 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase J.Mol.Biol., 351, 2005
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1WKI
| solution structure of ribosomal protein L16 from thermus thermophilus HB8 | Descriptor: | LSU ribosomal protein L16P | Authors: | Nishimura, M, Yoshida, T, Shirouzu, M, Terada, T, Kuramitsu, S, Yokoyama, S, Ohkubo, T, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-05-31 | Release date: | 2004-12-14 | Last modified: | 2011-07-13 | Method: | SOLUTION NMR | Cite: | Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8 J.Mol.Biol., 344, 2004
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1Y1B
| Solution structure of Anemonia elastase inhibitor | Descriptor: | Elastase inhibitor | Authors: | Hemmi, H, Kumazaki, T, Yoshizawa-Kumagaye, K, Nishiuchi, Y, Yoshida, T, Ohkubo, T, Kobayashi, Y. | Deposit date: | 2004-11-18 | Release date: | 2005-07-19 | Last modified: | 2022-03-02 | Method: | SOLUTION NMR | Cite: | Structural and Functional Study of an Anemonia Elastase Inhibitor, a "Nonclassical" Kazal-Type Inhibitor from Anemonia sulcata Biochemistry, 44, 2005
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1Y1C
| Solution structure of Anemonia elastase inhibitor analogue | Descriptor: | Elastase inhibitor | Authors: | Hemmi, H, Kumazaki, T, Yoshizawa-Kumagaye, K, Nishiuchi, Y, Yoshida, T, Ohkubo, T, Kobayashi, Y. | Deposit date: | 2004-11-18 | Release date: | 2005-07-19 | Last modified: | 2021-11-10 | Method: | SOLUTION NMR | Cite: | Structural and Functional Study of an Anemonia Elastase Inhibitor, a "Nonclassical" Kazal-Type Inhibitor from Anemonia sulcata Biochemistry, 44, 2005
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