8WT6
 
 | | Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange state | | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | | Deposit date: | 2023-10-18 | | Release date: | 2024-06-26 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Structural mechanism of bridge RNA-guided recombination.
Nature, 630, 2024
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8WT9
 | | Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction resolution) | | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | | Deposit date: | 2023-10-18 | | Release date: | 2024-06-26 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Structural mechanism of bridge RNA-guided recombination.
Nature, 630, 2024
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8X5V
 | | BlCas9-sgRNA-target DNA complex | | Descriptor: | 1,2-ETHANEDIOL, BlCas9, CHLORIDE ION, ... | | Authors: | Nakane, T, Nakagawa, R, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2023-11-19 | | Release date: | 2024-07-10 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure and engineering of Brevibacillus laterosporus Cas9.
Commun Biol, 7, 2024
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4U9L
 | | Structure of a membrane protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MAGNESIUM ION, Magnesium transporter MgtE | | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-08-06 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE
Nat Commun, 5, 2014
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4U9N
 | | Structure of a membrane protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MANGANESE (II) ION, Magnesium transporter MgtE, ... | | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-08-06 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE
Nat Commun, 5, 2014
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4Y7E
 | | Crystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose | | Descriptor: | CALCIUM ION, Endoglucanase, GLYCEROL, ... | | Authors: | Kumagai, Y, Yamashita, K, Okuyama, M, Hatanaka, T, Yao, M, Kimura, A. | | Deposit date: | 2015-02-14 | | Release date: | 2015-09-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition
Febs J., 282, 2015
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7CCS
 | | Consensus mutated xCT-CD98hc complex | | Descriptor: | 4F2 cell-surface antigen heavy chain, Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System | | Authors: | Oda, K, Lee, Y, Takemoto, M, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-06-17 | | Release date: | 2020-12-09 | | Last modified: | 2020-12-16 | | Method: | ELECTRON MICROSCOPY (6.2 Å) | | Cite: | Consensus mutagenesis approach improves the thermal stability of system x c - transporter, xCT, and enables cryo-EM analyses.
Protein Sci., 29, 2020
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7C7L
 | | Cryo-EM structure of the Cas12f1-sgRNA-target DNA complex | | Descriptor: | CRISPR-associated protein Cas14a.1, DNA (40-mer), ZINC ION, ... | | Authors: | Takeda, N.S, Nakagawa, R, Okazaki, S, Hirano, H, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2020-05-26 | | Release date: | 2020-12-23 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structure of the miniature type V-F CRISPR-Cas effector enzyme.
Mol.Cell, 81, 2021
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7XWS
 | | Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis with small volume | | Descriptor: | ACETYL GROUP, CHLORIDE ION, Polyhedrin | | Authors: | Abe, S, Tanaka, J, Kojima, M, Hirata, K, Yamashita, K, Ueno, T. | | Deposit date: | 2022-05-27 | | Release date: | 2023-02-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Cell-free protein crystallization for nanocrystal structure determination.
Sci Rep, 12, 2022
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8JHH
 | | Glycoside hydrolase family 55 endo-beta-1,3-glucanase from Microdochium nivale | | Descriptor: | GLYCEROL, MnLam55A | | Authors: | Ota, T, Saburi, W, Yamashita, K, Tagami, T, Yu, J, Komba, S, Jewell, L.E, Hsiang, T, Imai, R, Yao, M, Mori, H. | | Deposit date: | 2023-05-23 | | Release date: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Molecular mechanism for endo-type action of glycoside hydrolase family 55 endo-beta-1,3-glucanase on beta 1-3/1-6-glucan.
J.Biol.Chem., 299, 2023
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2N5J
 | | Regnase-1 N-terminal domain | | Descriptor: | Ribonuclease ZC3H12A | | Authors: | Yokogawa, M, Tsushima, T, Noda, N.N, Kumeta, H, Adachi, W, Enokizono, Y, Yamashita, K, Standley, D.M, Takeuchi, O, Akira, S, Inagaki, F. | | Deposit date: | 2015-07-18 | | Release date: | 2016-03-16 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Sci Rep, 6, 2016
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2N5K
 | | Regnase-1 Zinc finger domain | | Descriptor: | Ribonuclease ZC3H12A, ZINC ION | | Authors: | Yokogawa, M, Tsushima, T, Noda, N.N, Kumeta, H, Adachi, W, Enokizono, Y, Yamashita, K, Standley, D.M, Takeuchi, O, Akira, S, Inagaki, F. | | Deposit date: | 2015-07-18 | | Release date: | 2016-03-16 | | Last modified: | 2023-06-14 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Sci Rep, 6, 2016
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2OAZ
 | | Human Methionine Aminopeptidase-2 Complexed with SB-587094 | | Descriptor: | COBALT (II) ION, N-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE, human Methionine Amino Peptidase 2 | | Authors: | Marino Jr, J.P, Fisher, P.W, Hofmann, G.A, Kirkpatrick, R, Janson, C.A, Johnson, R.K, Ma, C, Mattern, M, Meek, T.D, Ryan, D, Schulz, C, Smith, W.W, Tew, D.G, Tomazek Jr, T.A, Veber, D.F, Xiong, W.C, Yamamoto, Y, Yamashita, K, Yang, G, Thompson, S.K. | | Deposit date: | 2006-12-18 | | Release date: | 2007-06-19 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Highly potent inhibitors of methionine aminopeptidase-2 based on a 1,2,4-triazole pharmacophore.
J.Med.Chem., 50, 2007
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2N5L
 | | Regnase-1 C-terminal domain | | Descriptor: | Ribonuclease ZC3H12A | | Authors: | Yokogawa, M, Tsushima, T, Noda, N.N, Kumeta, H, Adachi, W, Enokizono, Y, Yamashita, K, Standley, D.M, Takeuchi, O, Akira, S, Inagaki, F. | | Deposit date: | 2015-07-18 | | Release date: | 2016-03-16 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Sci Rep, 6, 2016
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5WS3
 | | Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA | | Descriptor: | N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, ... | | Authors: | Suno, R, Kimura, K, Nakane, T, Yamashita, K, Wang, J, Fujiwara, T, Yamanaka, Y, Im, D, Tsujimoto, H, Sasanuma, M, Horita, S, Hirokawa, T, Nango, E, Tono, K, Kameshima, T, Hatsui, T, Joti, Y, Yabashi, M, Shimamoto, K, Yamamoto, M, Rosenbaum, D.M, Iwata, S, Shimamura, T, Kobayashi, T. | | Deposit date: | 2016-12-05 | | Release date: | 2017-12-13 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.
Structure, 26, 2018
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5X93
 | | Human endothelin receptor type-B in complex with antagonist K-8794 | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 3-[6-[(4-tert-butylphenyl)sulfonylamino]-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]oxy-N-(2,6-dimethylphenyl)propanamide, CHOLESTEROL, ... | | Authors: | Shihoya, W, Nishizawa, T, Yamashita, K, Hirata, K, Okuta, A, Tani, K, Fujiyoshi, Y, Doi, T, Nureki, O. | | Deposit date: | 2017-03-05 | | Release date: | 2017-08-16 | | Last modified: | 2017-11-15 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog
Nat. Struct. Mol. Biol., 24, 2017
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5XPR
 | | Human endothelin receptor type-B in complex with antagonist bosentan | | Descriptor: | 4-tert-butyl-N-[6-(2-hydroxyethyloxy)-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]benzenesulfonamide, Endothelin B receptor,Endolysin,Endothelin B receptor, SULFATE ION | | Authors: | Shihoya, W, Nishizawa, T, Yamashita, K, Hirata, K, Okuta, A, Tani, K, Fujiyoshi, Y, Doi, T, Nureki, O. | | Deposit date: | 2017-06-04 | | Release date: | 2017-08-16 | | Last modified: | 2017-11-15 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog
Nat. Struct. Mol. Biol., 24, 2017
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5WQC
 | | Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8. | | Descriptor: | N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, ... | | Authors: | Suno, R, Hirata, K, Yamashita, K, Tsujimoto, H, Sasanuma, M, Horita, S, Yamamoto, M, Rosenbaum, D.M, Iwata, S, Shimamura, T, Kobayashi, T. | | Deposit date: | 2016-11-25 | | Release date: | 2017-11-29 | | Last modified: | 2018-01-17 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA
Structure, 26, 2018
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2A6V
 | | Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form | | Descriptor: | 1,2-ETHANEDIOL, Emp46p, POTASSIUM ION | | Authors: | Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S. | | Deposit date: | 2005-07-04 | | Release date: | 2006-01-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
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2A6Z
 | | Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1 | | Descriptor: | Emp47p (form2) | | Authors: | Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S. | | Deposit date: | 2005-07-04 | | Release date: | 2006-01-31 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
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2A6X
 | | Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant | | Descriptor: | 1,2-ETHANEDIOL, Emp46p, POTASSIUM ION | | Authors: | Satoh, T, Sato, K, Kanoh, A, Yamashita, K, Kato, R, Nakano, A, Wakatsuki, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-04 | | Release date: | 2006-01-31 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p.
J.Biol.Chem., 281, 2006
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8PVG
 | | Structure of E. coli glutamine synthetase determined by cryoEM at 100 keV | | Descriptor: | Glutamine synthetase | | Authors: | McMullan, G, Naydenova, K, Mihaylov, D, Peet, M.J, Wilson, H, Yamashita, K, Dickerson, J.L, Chen, S, Cannone, G, Lee, Y, Hutchings, K.A, Gittins, O, Sobhy, M, Wells, T, El-Gomati, M.M, Dalby, J, Meffert, M, Schulze-Briese, C, Henderson, R, Russo, C.J. | | Deposit date: | 2023-07-17 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structure determination by cryoEM at 100 keV.
Proc.Natl.Acad.Sci.USA, 120, 2023
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8PVC
 | | Structure of mouse heavy-chain apoferritin determined by cryoEM at 100 keV | | Descriptor: | FE (III) ION, Ferritin heavy chain, ZINC ION | | Authors: | McMullan, G, Naydenova, K, Mihaylov, D, Peet, M.J, Wilson, H, Yamashita, K, Dickerson, J.L, Chen, S, Cannone, G, Lee, Y, Hutchings, K.A, Gittins, O, Sobhy, M, Wells, T, El-Gomati, M.M, Dalby, J, Meffert, M, Schulze-Briese, C, Henderson, R, Russo, C.J. | | Deposit date: | 2023-07-17 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (2.6 Å) | | Cite: | Structure determination by cryoEM at 100 keV.
Proc.Natl.Acad.Sci.USA, 120, 2023
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8PVE
 | | Structure of AHIR determined by cryoEM at 100 keV | | Descriptor: | Ketol-acid reductoisomerase (NADP(+)) | | Authors: | McMullan, G, Naydenova, K, Mihaylov, D, Peet, M.J, Wilson, H, Yamashita, K, Dickerson, J.L, Chen, S, Cannone, G, Lee, Y, Hutchings, K.A, Gittins, O, Sobhy, M, Wells, T, El-Gomati, M.M, Dalby, J, Meffert, M, Schulze-Briese, C, Henderson, R, Russo, C.J. | | Deposit date: | 2023-07-17 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structure determination by cryoEM at 100 keV.
Proc.Natl.Acad.Sci.USA, 120, 2023
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8PVJ
 | | Structure of lumazine synthase determined by cryoEM at 100 keV | | Descriptor: | 6,7-dimethyl-8-ribityllumazine synthase | | Authors: | McMullan, G, Naydenova, K, Mihaylov, D, Peet, M.J, Wilson, H, Yamashita, K, Dickerson, J.L, Chen, S, Cannone, G, Lee, Y, Hutchings, K.A, Gittins, O, Sobhy, M, Wells, T, El-Gomati, M.M, Dalby, J, Meffert, M, Schulze-Briese, C, Henderson, R, Russo, C.J. | | Deposit date: | 2023-07-17 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structure determination by cryoEM at 100 keV.
Proc.Natl.Acad.Sci.USA, 120, 2023
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