3HJ7
 
 | | Crystal structure of TILS C-terminal domain | | Descriptor: | CHLORIDE ION, tRNA(Ile)-lysidine synthase | | Authors: | Nakanishi, K, Bonnefond, L, Kimura, S, Suzuki, T, Ishitani, R, Nureki, O. | | Deposit date: | 2009-05-21 | | Release date: | 2009-10-20 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
Nature, 461, 2009
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3DJN
 | | Crystal structure of mouse TIS21 | | Descriptor: | Protein BTG2 | | Authors: | Yang, X, Morita, M, Wang, H, Suzuki, T, Bartlam, M, Yamamoto, T. | | Deposit date: | 2008-06-24 | | Release date: | 2008-11-11 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity
Nucleic Acids Res., 36, 2008
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4XD7
 | | Structure of thermophilic F1-ATPase inhibited by epsilon subunit | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATP synthase epsilon chain, ATP synthase gamma chain, ... | | Authors: | SHIRAKIHARA, Y, SHIRATORI, A, TANIKAWA, H, NAKASAKO, M, YOSHIDA, M, SUZUKI, T. | | Deposit date: | 2014-12-19 | | Release date: | 2015-08-26 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (3.9 Å) | | Cite: | Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.
Febs J., 282, 2015
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7BPG
 | | Structure of serinol nucleic acid - RNA complex | | Descriptor: | CALCIUM ION, RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3'), SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R) | | Authors: | Kamiya, Y, Satoh, T, Kodama, A, Suzuki, T, Uchiyama, S, Kato, K, Asanuma, H. | | Deposit date: | 2020-03-22 | | Release date: | 2020-11-25 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Commun Chem, 2020
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7BPF
 | | Structure of L-threoninol nucleic acid - RNA complex | | Descriptor: | L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1'), RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3') | | Authors: | Kamiya, Y, Satoh, T, Kodama, A, Suzuki, T, Uchiyama, S, Kato, K, Asanuma, H. | | Deposit date: | 2020-03-22 | | Release date: | 2020-11-25 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Commun Chem, 2020
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2VQF
 | | Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding | | Descriptor: | 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | | Authors: | Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. | | Deposit date: | 2008-03-14 | | Release date: | 2008-04-29 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
J.Biol.Chem., 283, 2008
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2VQE
 | | Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U-G wobble pairing during decoding | | Descriptor: | 16S RRNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... | | Authors: | Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. | | Deposit date: | 2008-03-13 | | Release date: | 2008-04-29 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
J.Biol.Chem., 283, 2008
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4K7B
 | | Crystal structure of Extrinsic protein in photosystem II | | Descriptor: | Extrinsic protein in photosystem II, GLYCEROL, SULFATE ION | | Authors: | Nagao, R, Suga, M, Niikura, A, Okumura, A, Koua, F.H.M, Suzuki, T, Tomo, T, Enami, I, Shen, J.R. | | Deposit date: | 2013-04-16 | | Release date: | 2013-09-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal Structure of Psb31, a Novel Extrinsic Protein of Photosystem II from a Marine Centric Diatom and Implications for Its Binding and Function
Biochemistry, 52, 2013
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3OQH
 | | Crystal structure of B. licheniformis CDPS yvmC-BLIC | | Descriptor: | GLYCEROL, Putative uncharacterized protein yvmC | | Authors: | Bonnefond, L, Arai, T, Suzuki, T, Ishitani, R, Nureki, O. | | Deposit date: | 2010-09-03 | | Release date: | 2011-02-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.901 Å) | | Cite: | Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Proc.Natl.Acad.Sci.USA, 108, 2011
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3OQJ
 | | Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CAPSO | | Descriptor: | (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid, Putative uncharacterized protein yvmC | | Authors: | Bonnefond, L, Arai, T, Suzuki, T, Ishitani, R, Nureki, O. | | Deposit date: | 2010-09-03 | | Release date: | 2011-02-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.399 Å) | | Cite: | Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Proc.Natl.Acad.Sci.USA, 108, 2011
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3OQI
 | | Crystal structure of B. licheniformis CDPS yvmC-BLIC in complex with CHES | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, GLYCEROL, Putative uncharacterized protein yvmC | | Authors: | Bonnefond, L, Arai, T, Suzuki, T, Ishitani, R, Nureki, O. | | Deposit date: | 2010-09-03 | | Release date: | 2011-02-23 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Proc.Natl.Acad.Sci.USA, 108, 2011
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7WEM
 | | Solid-state NMR Structure of TFo c-Subunit Ring | | Descriptor: | ATP synthase subunit c | | Authors: | Akutsu, H, Todokoro, Y, Kang, S.-J, Suzuki, T, Yoshida, M, Ikegami, T, Fujiwara, T. | | Deposit date: | 2021-12-23 | | Release date: | 2022-08-10 | | Last modified: | 2024-05-15 | | Method: | SOLID-STATE NMR | | Cite: | Chemical Conformation of the Essential Glutamate Site of the c -Ring within Thermophilic Bacillus F o F 1 -ATP Synthase Determined by Solid-State NMR Based on its Isolated c -Ring Structure.
J.Am.Chem.Soc., 144, 2022
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7YH6
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-12 | | Release date: | 2023-07-19 | | Last modified: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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7YH7
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-13 | | Release date: | 2023-07-19 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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5CI9
 | | Crystal structure of human Tob in complex with inhibitor fragment 6 | | Descriptor: | 1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid, Protein Tob1, SODIUM ION | | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | | Deposit date: | 2015-07-11 | | Release date: | 2015-11-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach
Protein Cell, 6, 2015
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5CI8
 | | Crystal structure of human Tob in complex with inhibitor fragment 1 | | Descriptor: | Protein Tob1, pyrrolo[1,2-a]quinoxalin-4(5H)-one | | Authors: | Bai, Y, Tashiro, S, Nagatoishi, S, Suzuki, T, Tsumoto, K, Bartlam, M, Yamamoto, T. | | Deposit date: | 2015-07-11 | | Release date: | 2015-11-18 | | Last modified: | 2015-12-09 | | Method: | X-RAY DIFFRACTION (2.328 Å) | | Cite: | Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach
Protein Cell, 6, 2015
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7VNV
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7VNW
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7VNX
 | | Crystal structure of TkArkI | | Descriptor: | GUANOSINE, TkArkI | | Authors: | Yamashita, S, Minowa, K, Ohira, T, Suzuki, T, Tomita, K. | | Deposit date: | 2021-10-12 | | Release date: | 2022-05-04 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.801 Å) | | Cite: | Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Nature, 605, 2022
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1WTG
 | | Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-biphenylalanine-Gln-p-aminobenzamidine | | Descriptor: | 2-(3-BIPHENYL-4-YL-2-ETHANESULFONYLAMINO-PROPIONYLAMINO)-PENTANEDIOIC ACID 5-AMIDE 1-(4-CARBAMIMIDOYL-BENZYLAMIDE), CALCIUM ION, Coagulation factor VII, ... | | Authors: | Kadono, S, Sakamoto, S, Kikuchi, Y, Oh-Eda, M, Yabuta, N, Kitazawa, K, Yoshihashi, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Kodama, M, Haramura, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T. | | Deposit date: | 2004-11-23 | | Release date: | 2005-11-23 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Novel interactions of large P3 moiety and small P4 moiety in the binding of the peptide mimetic factor VIIa inhibitor
Biochem.Biophys.Res.Commun., 326, 2005
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8HGM
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, NIV-11 Fab light chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-11-15 | | Release date: | 2023-10-25 | | Last modified: | 2024-09-25 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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8HGL
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-11 Fab heavy chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-11-15 | | Release date: | 2023-10-25 | | Last modified: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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8HES
 | | Crystal structure of SARS-CoV-2 RBD and NIV-10 complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-10 Fab H-chain, NIV-10 Fab L-chain, ... | | Authors: | Moriyama, S, Anraku, Y, Taminishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-11-08 | | Release date: | 2023-11-08 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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8HU1
 | | E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and ct6A37 in classical state | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | | Deposit date: | 2022-12-22 | | Release date: | 2024-04-03 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (2.69 Å) | | Cite: | Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 31, 2024
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8HTZ
 | | E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | | Deposit date: | 2022-12-22 | | Release date: | 2024-04-03 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (2.4 Å) | | Cite: | Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 31, 2024
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