3G5Q
 
 | | Crystal structure of Thermus thermophilus TrmFO | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO | | Authors: | Nishimasu, H, Ishitani, R, Hori, H, Nureki, O. | | Deposit date: | 2009-02-05 | | Release date: | 2009-05-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.102 Å) | | Cite: | Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Proc.Natl.Acad.Sci.USA, 106, 2009
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3G5R
 | | Crystal structure of Thermus thermophilus TrmFO in complex with tetrahydrofolate | | Descriptor: | (6S)-5,6,7,8-TETRAHYDROFOLATE, 1,2-ETHANEDIOL, CALCIUM ION, ... | | Authors: | Nishimasu, H, Ishitani, R, Hori, H, Nureki, O. | | Deposit date: | 2009-02-05 | | Release date: | 2009-05-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Proc.Natl.Acad.Sci.USA, 106, 2009
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5Y5L
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5I
 | | Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5J
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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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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8H1J
 | | Cryo-EM structure of the TnpB-omegaRNA-target DNA ternary complex | | Descriptor: | Non-target strand, RNA-guided DNA endonuclease TnpB, Target strand, ... | | Authors: | Nakagawa, R, Hirano, H, Omura, S, Nureki, O. | | Deposit date: | 2022-10-03 | | Release date: | 2023-04-12 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Cryo-EM structure of the transposon-associated TnpB enzyme.
Nature, 616, 2023
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5Y5K
 | | Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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8GW8
 | | the human PTH1 receptor bound to an intracellular biased agonist | | Descriptor: | 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, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, ... | | Authors: | Kobayashi, K, Kusakizako, T, Okamoto, H.H, Nureki, O. | | Deposit date: | 2022-09-16 | | Release date: | 2023-06-14 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Class B1 GPCR activation by an intracellular agonist.
Nature, 618, 2023
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5XW6
 | | Crystal structure of the chicken ATP-gated P2X7 receptor channel in the presence of competitive antagonist TNP-ATP at 3.1 Angstroms | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, P2X purinoceptor, SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE | | Authors: | Kasuya, G, Hattori, M, Nureki, O. | | Deposit date: | 2017-06-29 | | Release date: | 2017-10-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structural insights into the competitive inhibition of the ATP-gated P2X receptor channel
Nat Commun, 8, 2017
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3VU8
 | | Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue | | Descriptor: | Methionine--tRNA ligase, N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE, ZINC ION | | Authors: | Konno, M, Kato-Murayama, M, Toma-Fukai, S, Uchikawa, E, Nureki, O, Yokoyama, S. | | Deposit date: | 2012-06-22 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases
To be Published
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8JEW
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8IY6
 | | ETB-Gi complex bound to Endotheline-1, focused on receptor | | Descriptor: | Endothelin type B receptor, Endothelin-1 | | Authors: | Sano, F.K, Akasaka, H, Shihoya, W, Nureki, O. | | Deposit date: | 2023-04-04 | | Release date: | 2023-08-16 | | Last modified: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (3.13 Å) | | Cite: | Cryo-EM structure of the endothelin-1-ET B -G i complex.
Elife, 12, 2023
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8IY5
 | | ETB-Gi complex bound to endothelin-1 | | Descriptor: | Endothelin type B receptor, Endothelin-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ... | | Authors: | Sano, F.K, Akasaka, H, Shihoya, W, Nureki, O. | | Deposit date: | 2023-04-04 | | Release date: | 2023-08-16 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Cryo-EM structure of the endothelin-1-ET B -G i complex.
Elife, 12, 2023
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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 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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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 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (2.95 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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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 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (2.91 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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5Y5M
 | | SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5CH4
 | | Peptide-Bound State of Thermus thermophilus SecYEG | | Descriptor: | Protein translocase subunit SecE, Protein translocase subunit SecY, Putative preprotein translocase, ... | | Authors: | Tanaka, Y, Sugano, Y, Takemoto, M, Kusakizako, T, Kumazaki, K, Ishitani, R, Nureki, O, Tsukazaki, T. | | Deposit date: | 2015-07-10 | | Release date: | 2015-11-25 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.64 Å) | | Cite: | Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State.
Cell Rep, 13, 2015
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5D4H
 | | High-resolution nitrite complex of a copper nitrite reductase determined by synchrotron radiation crystallography | | Descriptor: | ACETIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Fukuda, Y, Tse, K.M, Nakane, T, Nakatsu, T, Suzuki, M, Sugahara, M, Inoue, S, Masuda, T, Yumoto, F, Matsugaki, N, Nango, E, Tono, K, Joti, Y, Kameshima, T, Song, C, Hatsui, T, Yabashi, M, Nureki, O, Murphy, M.E.P, Inoue, T, Iwata, S, Mizohata, E. | | Deposit date: | 2015-08-07 | | Release date: | 2016-03-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Proc.Natl.Acad.Sci.USA, 113, 2016
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1JZQ
 | | Isoleucyl-tRNA synthetase Complexed with Isoleucyl-adenylate analogue | | Descriptor: | Isoleucyl-tRNA synthetase, N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, ZINC ION | | Authors: | Nakama, T, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-09-17 | | Release date: | 2001-12-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase.
J.Biol.Chem., 276, 2001
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7BTW
 | | The mitochondrial SAM complex from S.cere | | Descriptor: | Mitochondrial outer membrane beta-barrel protein, SAM37 isoform 1, Sorting assembly machinery 35 kDa subunit | | Authors: | Takeda, H, Tsutsumi, A, Nishizawa, T, Nureki, O, Kikkawa, M, Endo, T. | | Deposit date: | 2020-04-03 | | Release date: | 2021-01-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Mitochondrial sorting and assembly machinery operates by beta-barrel switching.
Nature, 590, 2021
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7BTX
 | | The mitochondrial SAM-Mdm10 supercomplex in GDN micelle from S.cere | | Descriptor: | MDM10 isoform 1, Mitochondrial outer membrane beta-barrel protein, Sorting assembly machinery 35 kDa subunit, ... | | Authors: | Takeda, H, Tsutsumi, A, Nishizawa, T, Nureki, O, Kikkawa, M, Endo, T. | | Deposit date: | 2020-04-03 | | Release date: | 2021-01-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Mitochondrial sorting and assembly machinery operates by beta-barrel switching.
Nature, 590, 2021
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