2Z3K
 
 | | complex structure of LF-transferase and rAF | | 分子名称: | 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL, D(-)-TARTARIC ACID, Leucyl/phenylalanyl-tRNA-protein transferase, ... | | 著者 | Watanabe, K, Toh, Y, Tomita, K. | | 登録日 | 2007-06-04 | | 公開日 | 2007-10-23 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.85 Å) | | 主引用文献 | Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449, 2007
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2Z3M
 | | complex structure of LF-transferase and dAF | | 分子名称: | (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol, D(-)-TARTARIC ACID, Leucyl/phenylalanyl-tRNA-protein transferase, ... | | 著者 | Watanabe, K, Toh, Y, Tomita, K. | | 登録日 | 2007-06-04 | | 公開日 | 2007-10-23 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.7 Å) | | 主引用文献 | Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449, 2007
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2Z3L
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2Z3N
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8ANY
 | | Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA | | 分子名称: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | 著者 | Singh, V, Itoh, Y, Amunts, A. | | 登録日 | 2022-08-06 | | 公開日 | 2023-08-16 | | 最終更新日 | 2024-06-26 | | 実験手法 | ELECTRON MICROSCOPY (2.85 Å) | | 主引用文献 | Structural basis of LRPPRC-SLIRP-dependent translation by the
mitoribosome
To Be Published
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7QI6
 | | Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution | | 分子名称: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | 著者 | Singh, V, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-14 | | 公開日 | 2023-05-17 | | 最終更新日 | 2024-07-31 | | 実験手法 | ELECTRON MICROSCOPY (2.98 Å) | | 主引用文献 | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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7QI5
 | | Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution | | 分子名称: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | 著者 | Singh, V, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-14 | | 公開日 | 2023-07-05 | | 最終更新日 | 2024-07-31 | | 実験手法 | ELECTRON MICROSCOPY (2.63 Å) | | 主引用文献 | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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7QI4
 | | Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA) | | 分子名称: | 1,4-DIAMINOBUTANE, 12S mitochondrial rRNA, 16S mitochondrial rRNA, ... | | 著者 | Singh, V, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-14 | | 公開日 | 2022-07-13 | | 最終更新日 | 2024-07-31 | | 実験手法 | ELECTRON MICROSCOPY (2.21 Å) | | 主引用文献 | Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Nat Commun, 15, 2024
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7QIY
 | | Specific features and methylation sites of a plant ribosome. 40S head ribosomal subunit. | | 分子名称: | 1,4-DIAMINOBUTANE, 18S rRNA head, 40S head ribosomal protein eS19, ... | | 著者 | Cottilli, P, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-16 | | 公開日 | 2022-06-15 | | 最終更新日 | 2024-04-24 | | 実験手法 | ELECTRON MICROSCOPY (2.58 Å) | | 主引用文献 | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIX
 | | Specific features and methylation sites of a plant ribosome. 40S body ribosomal subunit. | | 分子名称: | 18S rRNA body, 30S ribosomal protein S15, chloroplastic, ... | | 著者 | Cottilli, P, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-16 | | 公開日 | 2022-06-15 | | 最終更新日 | 2024-04-24 | | 実験手法 | ELECTRON MICROSCOPY (2.53 Å) | | 主引用文献 | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIW
 | | Specific features and methylation sites of a plant ribosome. 60S ribosomal subunit. | | 分子名称: | 25S rRNA, 5.8S rRNA, 50S ribosomal protein L22, ... | | 著者 | Cottilli, P, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-16 | | 公開日 | 2022-07-13 | | 最終更新日 | 2023-11-15 | | 実験手法 | ELECTRON MICROSCOPY (2.35 Å) | | 主引用文献 | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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7QIZ
 | | Specific features and methylation sites of a plant 80S ribosome | | 分子名称: | 1,4-DIAMINOBUTANE, 18S, 25S rRNA, ... | | 著者 | Cottilli, P, Itoh, Y, Amunts, A. | | 登録日 | 2021-12-16 | | 公開日 | 2022-08-03 | | 最終更新日 | 2024-04-24 | | 実験手法 | ELECTRON MICROSCOPY (2.38 Å) | | 主引用文献 | Cryo-EM structure and rRNA modification sites of a plant ribosome.
Plant Commun., 3, 2022
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3C7X
 | | Hemopexin-like domain of matrix metalloproteinase 14 | | 分子名称: | CHLORIDE ION, Matrix metalloproteinase-14, SODIUM ION | | 著者 | Tochowicz, A, Itoh, Y, Maskos, K, Bode, W, Goettig, P. | | 登録日 | 2008-02-08 | | 公開日 | 2009-02-10 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions
J.Biol.Chem., 286, 2011
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2N37
 | | Solution structure of AVR-Pia | | 分子名称: | AVR-Pia protein | | 著者 | Ose, T, Oikawa, A, Nakamura, Y, Maenaka, K, Higuchi, Y, Satoh, Y, Fujiwara, S, Demura, M, Sone, T. | | 登録日 | 2015-05-25 | | 公開日 | 2015-10-14 | | 最終更新日 | 2023-06-14 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution structure of an avirulence protein, AVR-Pia, from Magnaporthe oryzae
J.Biomol.Nmr, 63, 2015
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8YGJ
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt) | | 分子名称: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(P*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (51-MER), ... | | 著者 | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | 登録日 | 2024-02-26 | | 公開日 | 2024-06-05 | | 最終更新日 | 2024-07-17 | | 実験手法 | ELECTRON MICROSCOPY (3.2 Å) | | 主引用文献 | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUU
 | | SpCas9-pegRNA-target DNA complex (pre-initiation) | | 分子名称: | CRISPR-associated endonuclease Cas9/Csn1, DNA (34-MER), DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), ... | | 著者 | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | 登録日 | 2023-10-21 | | 公開日 | 2024-06-05 | | 最終更新日 | 2024-07-17 | | 実験手法 | ELECTRON MICROSCOPY (3.2 Å) | | 主引用文献 | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUS
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (termination) | | 分子名称: | CRISPR-associated endonuclease Cas9/Csn1, DNA (40-MER), DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), ... | | 著者 | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | 登録日 | 2023-10-21 | | 公開日 | 2024-06-05 | | 最終更新日 | 2024-07-17 | | 実験手法 | ELECTRON MICROSCOPY (2.9 Å) | | 主引用文献 | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUV
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt) | | 分子名称: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (50-MER), ... | | 著者 | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | 登録日 | 2023-10-21 | | 公開日 | 2024-06-05 | | 最終更新日 | 2024-07-17 | | 実験手法 | ELECTRON MICROSCOPY (3 Å) | | 主引用文献 | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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8WUT
 | | SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) | | 分子名称: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*TP*GP*AP*TP*GP*GP*CP*AP*GP*AP*GP*TP*AP*CP*TP*AP*G)-3'), DNA (51-MER), ... | | 著者 | Shuto, Y, Nakagawa, R, Hoki, M, Omura, S.N, Hirano, H, Itoh, Y, Nureki, O. | | 登録日 | 2023-10-21 | | 公開日 | 2024-06-05 | | 最終更新日 | 2024-07-17 | | 実験手法 | ELECTRON MICROSCOPY (3 Å) | | 主引用文献 | Structural basis for pegRNA-guided reverse transcription by a prime editor.
Nature, 631, 2024
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1WRD
 | | Crystal structure of Tom1 GAT domain in complex with ubiquitin | | 分子名称: | Target of Myb protein 1, Ubiquitin | | 著者 | Akutsu, M, Kawasaki, M, Katoh, Y, Shiba, T, Yamaguchi, Y, Kato, R, Kato, K, Nakayama, K, Wakatsuki, S. | | 登録日 | 2004-10-14 | | 公開日 | 2005-10-11 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.75 Å) | | 主引用文献 | Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.
Febs Lett., 579, 2005
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1WZZ
 | | Structure of endo-beta-1,4-glucanase CMCax from Acetobacter xylinum | | 分子名称: | Probable endoglucanase, SULFATE ION | | 著者 | Yasutake, Y, Kawano, S, Tajima, K, Yao, M, Satoh, Y, Munekata, M, Tanaka, I, Structural Genomics Consortium (SGC) | | 登録日 | 2005-03-10 | | 公開日 | 2006-03-14 | | 最終更新日 | 2011-07-13 | | 実験手法 | X-RAY DIFFRACTION (1.65 Å) | | 主引用文献 | Structural characterization of the Acetobacter xylinum endo-beta-1,4-glucanase CMCax required for cellulose biosynthesis.
Proteins, 64, 2006
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8J12
 | | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | | 分子名称: | DNA (38-MER), MAGNESIUM ION, RNA (247-MER), ... | | 著者 | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | 登録日 | 2023-04-12 | | 公開日 | 2023-09-27 | | 実験手法 | ELECTRON MICROSCOPY (3.08 Å) | | 主引用文献 | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J1J
 | | Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | | 分子名称: | DNA (38-MER), MAGNESIUM ION, RNA (118-MER), ... | | 著者 | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | 登録日 | 2023-04-13 | | 公開日 | 2023-09-27 | | 実験手法 | ELECTRON MICROSCOPY (2.91 Å) | | 主引用文献 | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J3R
 | | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | | 分子名称: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | | 著者 | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | 登録日 | 2023-04-18 | | 公開日 | 2023-09-27 | | 実験手法 | ELECTRON MICROSCOPY (2.95 Å) | | 主引用文献 | Minimal and most efficient genome editing Cas enzyme
To Be Published
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6J7C
 | | Crystal structure of proline racemase-like protein from Thermococcus litoralis in complex with proline | | 分子名称: | PROLINE, Proline racemase | | 著者 | Watanabe, Y, Watanabe, S, Itoh, Y, Watanabe, Y. | | 登録日 | 2019-01-17 | | 公開日 | 2019-02-27 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.7 Å) | | 主引用文献 | Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon.
Biochem. Biophys. Res. Commun., 511, 2019
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