8HIO
| Cryo-EM structure of the Cas12m2-crRNA binary complex | Descriptor: | Cas12m2, MAGNESIUM ION, RNA (56-MER), ... | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | Deposit date: | 2022-11-21 | Release date: | 2023-04-12 | Last modified: | 2023-08-30 | Method: | ELECTRON MICROSCOPY (3.73 Å) | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
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8HHM
| Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state | Descriptor: | Cas12m2, DNA (36-MER), MAGNESIUM ION, ... | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | Deposit date: | 2022-11-16 | Release date: | 2023-04-12 | Last modified: | 2024-05-22 | Method: | ELECTRON MICROSCOPY (3.08 Å) | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
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8HHL
| Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex | Descriptor: | Cas12m2, MAGNESIUM ION, NTS (36-MER), ... | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | Deposit date: | 2022-11-16 | Release date: | 2023-04-12 | Last modified: | 2023-08-30 | Method: | ELECTRON MICROSCOPY (2.87 Å) | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme. Nat.Struct.Mol.Biol., 30, 2023
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3E54
| Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA | Descriptor: | DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3'), ... | Authors: | Nomura, N, Nomura, Y, Sussman, D, Stoddard, B.L. | Deposit date: | 2008-08-13 | Release date: | 2008-12-30 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases Nucleic Acids Res., 36, 2008
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4YBQ
| Rat GLUT5 with Fv in the outward-open form | Descriptor: | Solute carrier family 2, facilitated glucose transporter member 5, antibody Fv fragment heavy chain, ... | Authors: | Nomura, N, Shimamura, T, Iwata, S. | Deposit date: | 2015-02-19 | Release date: | 2015-10-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.27 Å) | Cite: | Structure and mechanism of the mammalian fructose transporter GLUT5 Nature, 526, 2015
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6AAM
| Crystal structure of TYK2 in complex with peficitinib | Descriptor: | 4-[[(1S,3R)-5-oxidanyl-2-adamantyl]amino]-1H-pyrrolo[2,3-b]pyridine-5-carboxamide, Non-receptor tyrosine-protein kinase TYK2 | Authors: | Nomura, N, Tomimoto, Y. | Deposit date: | 2018-07-18 | Release date: | 2018-08-15 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | Discovery and structural characterization of peficitinib (ASP015K) as a novel and potent JAK inhibitor Bioorg. Med. Chem., 26, 2018
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8J1J
| Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (118-MER), ... | Authors: | 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. | Deposit date: | 2023-04-13 | Release date: | 2023-09-27 | Method: | ELECTRON MICROSCOPY (2.91 Å) | Cite: | 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 | Descriptor: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | Authors: | 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. | Deposit date: | 2023-04-18 | Release date: | 2023-09-27 | Method: | ELECTRON MICROSCOPY (2.95 Å) | Cite: | Minimal and most efficient genome editing Cas enzyme To Be Published
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8J12
| Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (247-MER), ... | Authors: | 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. | Deposit date: | 2023-04-12 | Release date: | 2023-09-27 | Method: | ELECTRON MICROSCOPY (3.08 Å) | Cite: | Minimal and most efficient genome editing Cas enzyme To Be Published
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7FCI
| human NTCP in complex with YN69083 Fab | Descriptor: | Fab Heavy chain, Fab Light chain, Sodium/bile acid cotransporter | Authors: | Park, J.H, Iwamoto, M, Yun, J.H, Uchikubo-Kamo, T, Son, D, Jin, Z, Yoshida, H, Ohki, M, Ishimoto, N, Mizutani, K, Oshima, M, Muramatsu, M, Wakita, T, Shirouzu, M, Liu, K, Uemura, T, Nomura, N, Iwata, S, Watashi, K, Tame, J.R.H, Nishizawa, T, Lee, W, Park, S.Y. | Deposit date: | 2021-07-14 | Release date: | 2022-05-25 | Last modified: | 2022-07-13 | Method: | ELECTRON MICROSCOPY (3.3 Å) | Cite: | Structural insights into the HBV receptor and bile acid transporter NTCP. Nature, 606, 2022
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2DCH
| Crystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I | Descriptor: | CHLORIDE ION, SULFATE ION, putative homing endonuclease | Authors: | Nakayama, H, Tsuge, H, Shimamura, T, Miyano, M, Nomura, N, Sako, Y. | Deposit date: | 2006-01-06 | Release date: | 2006-07-06 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability. J.Mol.Biol., 365, 2007
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2Z4F
| Solution structure of the Discoidin Domain of DDR2 | Descriptor: | Discoidin domain-containing receptor 2 | Authors: | Ichikawa, O, Osawa, M, Nishida, N, Goshima, N, Nomura, N, Shimada, I. | Deposit date: | 2007-06-16 | Release date: | 2007-09-04 | Last modified: | 2022-03-16 | Method: | SOLUTION NMR | Cite: | Structural basis of the collagen-binding mode of discoidin domain receptor 2 Embo J., 26, 2007
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5B8C
| High resolution structure of the human PD-1 in complex with pembrolizumab Fv | Descriptor: | Pembrolizumab heavy chain variable region (PemVH), Pembrolizumab light chain variable region (PemVL), Programmed cell death protein 1 | Authors: | Horita, S, Shimamura, T, Iwata, S, Nomura, N. | Deposit date: | 2016-06-14 | Release date: | 2016-10-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.146 Å) | Cite: | High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1 Sci Rep, 6, 2016
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7D7M
| Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein | Descriptor: | (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | Authors: | Nojima, S, Fujita, Y, Kimura, T.K, Nomura, N, Suno, R, Morimoto, K, Yamamoto, M, Noda, T, Iwata, S, Shigematsu, H, Kobayashi, T. | Deposit date: | 2020-10-05 | Release date: | 2020-11-18 | Last modified: | 2021-03-17 | Method: | ELECTRON MICROSCOPY (3.3 Å) | Cite: | Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein. Structure, 29, 2021
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6A94
| Crystal structure of 5-HT2AR in complex with zotepine | Descriptor: | 2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-(3-chloranylbenzo[b][1]benzothiepin-5-yl)oxy-N,N-dimethyl-ethanamine, 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562, ... | Authors: | Kimura, T.K, Asada, H, Inoue, A, Kadji, F.M.N, Im, D, Mori, C, Arakawa, T, Hirata, K, Nomura, Y, Nomura, N, Aoki, J, Iwata, S, Shimamura, T. | Deposit date: | 2018-07-11 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine. Nat.Struct.Mol.Biol., 26, 2019
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6A93
| Crystal structure of 5-HT2AR in complex with risperidone | Descriptor: | 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one, 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562, CHOLESTEROL, ... | Authors: | Kimura, T.K, Asada, H, Inoue, A, Kadji, F.M.N, Im, D, Mori, C, Arakawa, T, Hirata, K, Nomura, Y, Nomura, N, Aoki, J, Iwata, S, Shimamura, T. | Deposit date: | 2018-07-11 | Release date: | 2019-02-13 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine. Nat.Struct.Mol.Biol., 26, 2019
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5YOY
| Crystal structure of the human tumor necrosis factor in complex with golimumab Fv | Descriptor: | Golimumab heavy chain variable region, Golimumab light chain variable region, Tumor necrosis factor | Authors: | Ono, M, Horita, S, Sato, Y, Nomura, Y, Iwata, S, Nomura, N. | Deposit date: | 2017-10-31 | Release date: | 2018-05-09 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.727 Å) | Cite: | Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab Protein Sci., 27, 2018
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3A1Y
| The structure of archaeal ribosomal stalk P1/P0 complex | Descriptor: | 50S ribosomal protein P1 (L12P), Acidic ribosomal protein P0 | Authors: | Naganuma, T, Yao, M, Nomura, N, Yu, J, Uchiumi, T, Tanaka, I. | Deposit date: | 2009-04-25 | Release date: | 2009-11-17 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.13 Å) | Cite: | Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes J.Biol.Chem., 285, 2010
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3VG9
| Crystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 2.7 A resolution | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a, DODECYL-BETA-D-MALTOSIDE, ... | Authors: | Hino, T, Arakawa, T, Iwanari, H, Yurugi-Kobayashi, T, Ikeda-Suno, C, Nakada-Nakura, Y, Kusano-Arai, O, Weyand, S, Shimamura, T, Nomura, N, Cameron, A.D, Kobayashi, T, Hamakubo, T, Iwata, S, Murata, T. | Deposit date: | 2011-08-04 | Release date: | 2012-02-01 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody Nature, 482, 2012
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3VGA
| Crystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 3.1 A resolution | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a, antibody fab fragment heavy chain, ... | Authors: | Hino, T, Arakawa, T, Iwanari, H, Yurugi-Kobayashi, T, Ikeda-Suno, C, Nakada-Nakura, Y, Kusano-Arai, O, Weyand, S, Shimamura, T, Nomura, N, Cameron, A.D, Kobayashi, T, Hamakubo, T, Iwata, S, Murata, T. | Deposit date: | 2011-08-04 | Release date: | 2012-02-01 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody Nature, 482, 2012
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