8JLD
| Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2024-10-16 | Method: | ELECTRON MICROSCOPY (2.48 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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8JLA
| Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2023-11-08 | Method: | ELECTRON MICROSCOPY (3.44 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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8J9F
| Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1) | Descriptor: | Beta-glucosidase, GLYCEROL | Authors: | Yanai, T, Imaizumi, R, Takahashi, Y, Katsumura, E, Yamamoto, M, Nakayama, T, Yamashita, S, Takeshita, K, Sakai, N, Matsuura, H. | Deposit date: | 2023-05-03 | Release date: | 2024-04-10 | Last modified: | 2024-07-17 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Structural insights into a bacterial beta-glucosidase capable of degrading sesaminol triglucoside to produce sesaminol: toward the understanding of the aglycone recognition mechanism by the C-terminal lid domain. J.Biochem., 174, 2023
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6IMU
| The apo-structure of endo-beta-1,2-glucanase from Talaromyces funiculosus | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CITRIC ACID, DI(HYDROXYETHYL)ETHER, ... | Authors: | Tanaka, N, Nakajima, M, Narukawa-Nara, M, Matsunaga, H, Kamisuki, S, Aramasa, H, Takahashi, Y, Sugimoto, N, Abe, K, Miyanaga, A, Yamashita, T, Sugawara, F, Kamakura, T, Komba, S, Nakai, H, Taguchi, H. | Deposit date: | 2018-10-23 | Release date: | 2019-04-10 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family. J.Biol.Chem., 294, 2019
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6IMV
| The complex structure of endo-beta-1,2-glucanase from Talaromyces funiculosus with sophorose | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, ... | Authors: | Tanaka, N, Nakajima, M, Narukawa-Nara, M, Matsunaga, H, Kamisuki, S, Aramasa, H, Takahashi, Y, Sugimoto, N, Abe, K, Miyanaga, A, Yamashita, T, Sugawara, F, Kamakura, T, Komba, S, Nakai, H, Taguchi, H. | Deposit date: | 2018-10-23 | Release date: | 2019-04-10 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family. J.Biol.Chem., 294, 2019
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6IMW
| The complex structure of endo-beta-1,2-glucanase mutant (E262Q) from Talaromyces funiculosus with beta-1,2-glucan | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, Endo-beta-1,2-glucanase, ... | Authors: | Tanaka, N, Nakajima, M, Narukawa-Nara, M, Matsunaga, H, Kamisuki, S, Aramasa, H, Takahashi, Y, Sugimoto, N, Abe, K, Miyanaga, A, Yamashita, T, Sugawara, F, Kamakura, T, Komba, S, Nakai, H, Taguchi, H. | Deposit date: | 2018-10-23 | Release date: | 2019-04-10 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family. J.Biol.Chem., 294, 2019
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5H1R
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8JVC
| Crystal structure of dephospho-coenzyme A kinase | Descriptor: | GTP-dependent dephospho-CoA kinase | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | Deposit date: | 2023-06-28 | Release date: | 2024-06-19 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins, 92, 2024
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8JVG
| Crystal structure of dephospho-coenzyme A kinase | Descriptor: | GTP-dependent dephospho-CoA kinase | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | Deposit date: | 2023-06-28 | Release date: | 2024-06-19 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins, 92, 2024
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2ZW3
| Structure of the connexin-26 gap junction channel at 3.5 angstrom resolution | Descriptor: | Gap junction beta-2 protein | Authors: | Maeda, S, Nakagawa, S, Suga, M, Yamashita, E, Oshima, A, Fujiyoshi, Y, Tsukihara, T. | Deposit date: | 2008-12-01 | Release date: | 2009-04-07 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | Structure of the connexin 26 gap junction channel at 3.5 A resolution Nature, 458, 2009
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8JOG
| solution structure of Ras Binding Domein (RBD) in C-RAF with negative allosteric modulator. | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | Deposit date: | 2023-06-07 | Release date: | 2024-06-12 | Method: | SOLUTION NMR | Cite: | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers To Be Published
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8JOF
| solution-structure of Ras Binding Domain (RBD) in C-RAF | Descriptor: | RAF proto-oncogene serine/threonine-protein kinase | Authors: | Makino, Y, Matsumoto, S, Yoshikawa, Y, Kawamura, T, Kumasaka, T, Shima, F. | Deposit date: | 2023-06-07 | Release date: | 2024-06-12 | Method: | SOLUTION NMR | Cite: | Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers To Be Published
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8JVF
| Crystal structure of dephospho-coenzyme A kinase | Descriptor: | GTP-dependent dephospho-CoA kinase, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION | Authors: | Kita, A, Ishida, Y, Shimosaka, T, Michimori, Y, Makarova, K, Koonin, E, Atomi, H, Miki, K. | Deposit date: | 2023-06-28 | Release date: | 2024-06-19 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins, 92, 2024
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5H1Q
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5GUW
| Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa | Descriptor: | CALCIUM ION, CHLORIDE ION, FE (III) ION, ... | Authors: | Terasaka, E, Sugimoto, H, Shiro, Y, Tosha, T. | Deposit date: | 2016-08-31 | Release date: | 2017-08-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Dynamics of nitric oxide controlled by protein complex in bacterial system Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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4GRV
| The crystal structure of the neurotensin receptor NTS1 in complex with neurotensin (8-13) | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Neurotensin 8-13, Neurotensin receptor type 1, ... | Authors: | Noinaj, N, White, J.F, Shibata, Y, Love, J, Kloss, B, Xu, F, Gvozdenovic-Jeremic, J, Shah, P, Shiloach, J, Tate, C.G, Grisshammer, R. | Deposit date: | 2012-08-27 | Release date: | 2012-10-17 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.802 Å) | Cite: | Structure of the agonist-bound neurotensin receptor. Nature, 490, 2012
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7DVU
| Crystal structure of heme sensor protein PefR in complex with heme and cyanide | Descriptor: | CYANIDE ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | Deposit date: | 2021-01-15 | Release date: | 2021-09-29 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival. Commun Biol, 4, 2021
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7DVT
| Crystal structure of heme sensor protein PefR in complex with heme and carbon monoxide | Descriptor: | CARBON MONOXIDE, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | Deposit date: | 2021-01-15 | Release date: | 2021-09-29 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival. Commun Biol, 4, 2021
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7DVR
| Crystal structure of heme sensor protein PefR from Streptococcus agalactiae in complex with heme | Descriptor: | COBALT (II) ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | Deposit date: | 2021-01-15 | Release date: | 2021-09-29 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival. Commun Biol, 4, 2021
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7DVV
| Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer) | Descriptor: | DNA (28-MER), HTH marR-type domain-containing protein | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | Deposit date: | 2021-01-15 | Release date: | 2021-09-29 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.49 Å) | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival. Commun Biol, 4, 2021
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6JI2
| Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex | Descriptor: | Archaeal ribosomal stalk protein aP1, Elongation factor 1-alpha, GUANOSINE-5'-TRIPHOSPHATE, ... | Authors: | Maruyama, K, Imai, H, Kawamura, M, Ishino, S, Ishino, Y, Ito, K, Uchiumi, T. | Deposit date: | 2019-02-20 | Release date: | 2019-11-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations. Sci Rep, 9, 2019
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7E5P
| Aptamer enhancing peroxidase activity of myoglobin | Descriptor: | DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') | Authors: | Tsukakoshi, K, Matsugami, A, Khunathai, K, Kanazashi, M, Yamagishi, Y, Nakama, K, Oshikawa, D, Hayashi, F, Kuno, H, Ikebukuro, K. | Deposit date: | 2021-02-19 | Release date: | 2021-06-16 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol. Nucleic Acids Res., 49, 2021
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2LCF
| Solution structure of GppNHp-bound H-RasT35S mutant protein | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | Authors: | Araki, M, Shima, F, Yoshikawa, Y, Muraoka, S, Ijiri, Y, Nagahara, Y, Shirono, T, Kataoka, T, Tamura, A. | Deposit date: | 2011-04-28 | Release date: | 2011-09-28 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers. J.Biol.Chem., 286, 2011
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1JF5
| CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 2 MUTANT F286A | Descriptor: | ALPHA AMYLASE II, CALCIUM ION | Authors: | Ohtaki, A, Kondo, S, Shimura, Y, Tonozuka, T, Sakano, Y, Kamitori, S. | Deposit date: | 2001-06-20 | Release date: | 2002-05-22 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs CARBOHYDR.RES., 334, 2001
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1K2G
| Structural basis for the 3'-terminal guanosine recognition by the group I intron | Descriptor: | 5'-R(*CP*AP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*GP*CP*AP*GP*AP*GP*AP*UP*GP*G)-3' | Authors: | Kitamura, Y, Muto, Y, Watanabe, S, Kim, I, Ito, T, Nishiya, Y, Sakamoto, K, Ohtsuki, T, Kawai, G, Watanabe, K, Hosono, K, Takaku, H, Katoh, E, Yamazaki, T, Inoue, T, Yokoyama, S. | Deposit date: | 2001-09-27 | Release date: | 2002-05-08 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron. RNA, 8, 2002
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