3PUA
 
 | | PHF2 Jumonji-NOG-Ni(II) | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, N-OXALYLGLYCINE, ... | | Authors: | Horton, J.R, Upadhyay, A.K, Hashimoto, H, Zhang, X, Cheng, X. | | Deposit date: | 2010-12-03 | | Release date: | 2011-01-26 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Structural basis for human PHF2 Jumonji domain interaction with metal ions.
J.Mol.Biol., 406, 2011
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4GTY
 | | Crystal structure of mouse Enpp1 in complex with GMP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Kato, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2012-08-29 | | Release date: | 2012-11-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.19 Å) | | Cite: | Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Proc.Natl.Acad.Sci.USA, 109, 2012
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4GTW
 | | Crystal structure of mouse Enpp1 in complex with AMP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE MONOPHOSPHATE, ... | | Authors: | Kato, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2012-08-29 | | Release date: | 2012-11-07 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Proc.Natl.Acad.Sci.USA, 109, 2012
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4GTX
 | | Crystal structure of mouse Enpp1 in complex with TMP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Kato, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2012-08-29 | | Release date: | 2012-11-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.201 Å) | | Cite: | Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Proc.Natl.Acad.Sci.USA, 109, 2012
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2E8S
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION | | Authors: | Asada, Y, Shimada, H, Taketa, M, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-01-23 | | Release date: | 2007-07-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3
To be Published
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3R1M
 | | Structure of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase (aldolase form) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 1,3-DIHYDROXYACETONEPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Fushinobu, S, Nishimasu, H, Hattori, D, Song, H.-J, Wakagi, T. | | Deposit date: | 2011-03-10 | | Release date: | 2011-10-12 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase.
Nature, 478, 2011
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2EK4
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L8M) | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | | Authors: | Asada, Y, Shimada, H, Taketa, M, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-22 | | Release date: | 2007-09-25 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L8M)
To be Published
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2EK3
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L3M) | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | | Authors: | Asada, Y, Shimada, H, Taketa, M, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-22 | | Release date: | 2007-09-25 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L3M)
To be Published
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2EL3
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L242M) | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | | Authors: | Asada, Y, Matsuura, Y, Ono, N, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-26 | | Release date: | 2007-10-02 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L242M)
To be Published
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3PU3
 | | PHF2 Jumonji domain-NOG complex | | Descriptor: | 1,2-ETHANEDIOL, GLYCEROL, N-OXALYLGLYCINE, ... | | Authors: | Horton, J.R, Upadhyay, A.K, Hashimoto, H, Zhang, X, Cheng, X. | | Deposit date: | 2010-12-03 | | Release date: | 2011-01-26 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural basis for human PHF2 Jumonji domain interaction with metal ions.
J.Mol.Biol., 406, 2011
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2E8R
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION | | Authors: | Asada, Y, Taketa, M, Shimada, H, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-01-23 | | Release date: | 2007-07-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3
To be Published
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2EL0
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L21M) | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Asada, Y, Matsuura, Y, Ono, N, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-26 | | Release date: | 2007-10-02 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L21M)
To be Published
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2E8Q
 | | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (K19M) | | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Asada, Y, Shimada, H, Taketa, M, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-01-23 | | Release date: | 2007-07-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (K19M)
To be Published
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7VTI
 | | Crystal structure of the Cas13bt3-crRNA binary complex | | Descriptor: | 1,2-ETHANEDIOL, BROMIDE ION, CHLORIDE ION, ... | | Authors: | Nakagawa, R, Takeda, N.S, Tomita, A, Hirano, H, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2021-10-29 | | Release date: | 2022-08-24 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Structure and engineering of the minimal type VI CRISPR-Cas13bt3.
Mol.Cell, 82, 2022
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7VTN
 | | Cryo-EM structure of the Cas13bt3-crRNA-target RNA ternary complex | | Descriptor: | Cas13bt3, crRNA, target RNA | | Authors: | Nakagawa, R, Soumya, K, Han, A, Takeda, N.S, Tomita, A, Hirano, H, Kusakizako, T, Tomohiro, N, Yamashita, K, Feng, Z, Nishimasu, H, Nureki, O. | | Deposit date: | 2021-10-30 | | Release date: | 2022-09-07 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (3.38 Å) | | Cite: | Structure and engineering of the minimal type VI CRISPR-Cas13bt3.
Mol.Cell, 82, 2022
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7W86
 | | Crystal structure of the DYW domain of DYW1 | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, GLYCEROL, ... | | Authors: | Sawada, Y, Shimizu, H, Toma-Fukai, S, Shimizu, T. | | Deposit date: | 2021-12-07 | | Release date: | 2022-12-14 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.
Plant Cell, 35, 2023
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7X87
 | | The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophotetraose observed as sophorose | | Descriptor: | Beta-galactosidase, CALCIUM ION, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose | | Authors: | Kobayashi, K, Shimizu, H, Tanaka, N, Kuramochi, K, Nakai, H, Nakajima, M, Taguchi, H. | | Deposit date: | 2022-03-11 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages.
J Biol Chem, 298, 2022
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5YY3
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5YY2
 | | Crystal structure of AsqI with Zn | | Descriptor: | Uncharacterized protein AsqI, ZINC ION | | Authors: | Hara, K, Hashimoto, H, Kishimoto, S, Watanabe, K. | | Deposit date: | 2017-12-07 | | Release date: | 2018-08-01 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.91 Å) | | Cite: | Enzymatic one-step ring contraction for quinolone biosynthesis.
Nat Commun, 9, 2018
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7XZR
 | | Crystal structure of TNIK-AMPPNP-thiopeptide TP15 complex | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, SULFATE ION, ... | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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7XZQ
 | | Crystal structure of TNIK-thiopeptide TP1 complex | | Descriptor: | 1,4-BUTANEDIOL, TRAF2 and NCK-interacting protein kinase, thiopeptide TP1 | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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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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3I4D
 | | Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1 | | Descriptor: | (2R,3S)-heptane-1,2,3-triol, 1,4-DIETHYLENE DIOXIDE, BACTERIOCHLOROPHYLL A, ... | | Authors: | Fujii, R, Adachi, S, Roszak, A.W, Gardiner, A.T, Cogdell, R.J, Isaacs, N.W, Koshihara, S, Hashimoto, H. | | Deposit date: | 2009-07-01 | | Release date: | 2010-12-01 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography
To be Published
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5XUZ
 | | Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (CCCA PAM) | | Descriptor: | 1,2-ETHANEDIOL, DNA (29-MER), DNA (5'-D(*CP*GP*TP*CP*CP*CP*CP*CP*A)-3'), ... | | Authors: | Yamano, T, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2017-06-26 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.
Mol. Cell, 67, 2017
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8W7D
 | | Crystal structure of EcPPAT-FR901483 complex | | Descriptor: | Amidophosphoribosyltransferase, [(1S,3S,6S,7S,8R,9S)-6-[(4-methoxyphenyl)methyl]-3-(methylamino)-7-oxidanyl-5-azatricyclo[6.3.1.0^1,5]dodecan-9-yl] dihydrogen phosphate | | Authors: | Hara, K, Hashimoto, H, Nakahara, M, Sato, M, Watanabe, K. | | Deposit date: | 2023-08-30 | | Release date: | 2023-12-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.81 Å) | | Cite: | Uncommon Arrangement of Self-resistance Allows Biosynthesis of de novo Purine Biosynthesis Inhibitor that Acts as an Immunosuppressor.
J.Am.Chem.Soc., 145, 2023
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