6JO6
 
 | | Structure of the green algal photosystem I supercomplex with light-harvesting complex I | | Descriptor: | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Miyazaki, N, Takahashi, Y. | | Deposit date: | 2019-03-20 | | Release date: | 2019-06-19 | | Last modified: | 2019-06-26 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I.
Nat.Plants, 5, 2019
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7F4Z
 | | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with ADP | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, CHLORIDE ION, Heat shock 70 kDa protein 1B, ... | | Authors: | Yokoyama, T, Fujii, S, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2021-06-21 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.
Iucrj, 9, 2022
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7F50
 | | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with AMPPnP | | Descriptor: | CHLORIDE ION, Heat shock 70 kDa protein 1B, MAGNESIUM ION, ... | | Authors: | Yokoyama, T, Fujii, S, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2021-06-21 | | Release date: | 2022-06-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.703 Å) | | Cite: | Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.
Iucrj, 9, 2022
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6JO5
 | | Structure of the green algal photosystem I supercomplex with light-harvesting complex I | | Descriptor: | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Miyazaki, N, Takahashi, Y. | | Deposit date: | 2019-03-20 | | Release date: | 2019-06-19 | | Last modified: | 2019-06-26 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I.
Nat.Plants, 5, 2019
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6K0T
 | | Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-17 | | Descriptor: | 3-[(1~{E})-1-[8-[(8-chloranyl-2-cyclopropyl-imidazo[1,2-a]pyridin-3-yl)methyl]-3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene]ethyl]-4~{H}-1,2,4-oxadiazol-5-one, Peroxisome proliferator-activated receptor gamma, Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | | Authors: | Suzuki, M, Yamamoto, K, Takahashi, Y, Saito, J. | | Deposit date: | 2019-05-07 | | Release date: | 2019-10-30 | | Last modified: | 2019-11-06 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Development of a novel class of peroxisome proliferator-activated receptor (PPAR) gamma ligands as an anticancer agent with a unique binding mode based on a non-thiazolidinedione scaffold.
Bioorg.Med.Chem., 27, 2019
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6L4P
 | | Crystal structure of the complex between the axonemal outer-arm dynein light chain-1 and microtubule binding domain of gamma heavy chain | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Dynein light chain 1, axonemal, ... | | Authors: | Toda, A, Nishikawa, Y, Tanaka, H, Yagi, T, Kurisu, G. | | Deposit date: | 2019-10-19 | | Release date: | 2020-02-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.703 Å) | | Cite: | The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the gamma heavy chain shows how axonemal dynein tunes ciliary beating.
J.Biol.Chem., 295, 2020
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6L1X
 | | Quinol-dependent nitric oxide reductase (qNOR) from Neisseria meningitidis in the monomeric oxidized state with zinc complex. | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric-oxide reductase, ... | | Authors: | Jamali, M.M.A, Antonyuk, S.V, Tosha, T, Muramoto, K, Hasnain, S.S, Shiro, Y. | | Deposit date: | 2019-10-01 | | Release date: | 2020-04-01 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.15 Å) | | Cite: | The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.
Iucrj, 7, 2020
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6LCQ
 | | Crystal structure of rice defensin OsAFP1 | | Descriptor: | Defensin-like protein CAL1, PHOSPHATE ION | | Authors: | Ochiai, A, Ogawa, K, Fukuda, M, Suzuki, M, Ito, K, Tanaka, T, Sagehashi, Y, Taniguchi, M. | | Deposit date: | 2019-11-19 | | Release date: | 2020-04-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.62 Å) | | Cite: | Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding.
J.Biosci.Bioeng., 130, 2020
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6L3H
 | | Cryo-EM structure of dimeric quinol dependent Nitric Oxide Reductase (qNOR) from the pathogen Neisseria meninigitidis | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric-oxide reductase, ... | | Authors: | Jamali, M.M.A, Gopalasingam, C.C, Johnson, R.M, Tosha, T, Muench, S.P, Muramoto, K, Antonyuk, S.V, Shiro, Y, Hasnain, S.S. | | Deposit date: | 2019-10-11 | | Release date: | 2020-04-01 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.06 Å) | | Cite: | The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.
Iucrj, 7, 2020
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6K5W
 | | Solution structure of the chromodomain of yeast Eaf3 | | Descriptor: | Chromatin modification-related protein EAF3 | | Authors: | Okuda, M, Nishimura, Y. | | Deposit date: | 2019-05-31 | | Release date: | 2020-02-26 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | The Eaf3 chromodomain acts as a pH sensor for gene expression by altering its binding affinity for histone methylated-lysine residues.
Biosci.Rep., 40, 2020
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6MSP
 | | De novo Designed Protein Foldit3 | | Descriptor: | De novo Designed Protein Foldit3 | | Authors: | Liu, G, Ishida, Y, Swapna, G.V.T, Kleinfelter, S, Koepnick, B, Baker, D, Montelione, G.T. | | Deposit date: | 2018-10-17 | | Release date: | 2019-06-12 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | De novo protein design by citizen scientists.
Nature, 570, 2019
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3CV9
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R73A/R84A mutant) in complex with 1alpha,25-dihydroxyvitamin D3 | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
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3CV8
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant) | | Descriptor: | Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Hayashi, K, Sugimoto, H, Shinkyo, R, Yamada, M, Ikeda, S, Ikushiro, S, Kamakura, M, Shiro, Y, Sakaki, T. | | Deposit date: | 2008-04-18 | | Release date: | 2008-11-04 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Biochemistry, 47, 2008
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5X18
 | | Crystal structure of Casein kinase I homolog 1 | | Descriptor: | Casein kinase I homolog 1, GLYCEROL, MALONIC ACID | | Authors: | Kikuchi, M, Shinohara, Y, Ueda, H.R, Umehara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock
Mol. Cell, 67, 2017
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1UFM
 | | Solution structure of the PCI domain | | Descriptor: | COP9 complex subunit 4 | | Authors: | Suzuki, S, Hatanaka, H, Kigawa, T, Shirouzu, M, Hayashizaki, Y, The RIKEN Genome Exploration Research Group Phase I & II Teams, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-06-02 | | Release date: | 2004-06-29 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the PCI domain
To be Published
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3A31
 | | Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative) | | Descriptor: | Probable threonyl-tRNA synthetase 1, SULFATE ION, ZINC ION | | Authors: | Shimizu, S, Juan, E.C.M, Miyashita, Y, Sato, Y, Hoque, M.M, Suzuki, K, Yogiashi, M, Tsunoda, M, Dock-Bregeon, A.-C, Moras, D, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2009-06-07 | | Release date: | 2009-10-27 | | Last modified: | 2013-11-20 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain
J.Mol.Biol., 394, 2009
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3A32
 | | Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix | | Descriptor: | Probable threonyl-tRNA synthetase 1, SULFATE ION, ZINC ION | | Authors: | Shimizu, S, Juan, E.C.M, Miyashita, Y, Sato, Y, Hoque, M.M, Suzuki, K, Yogiashi, M, Tsunoda, M, Dock-Bregeon, A.-C, Moras, D, Sekiguchi, T, Takenaka, A. | | Deposit date: | 2009-06-07 | | Release date: | 2009-10-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain
J.Mol.Biol., 394, 2009
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1UHU
 | | Solution structure of the retroviral Gag MA-like domain of RIKEN cDNA 3110009E22 | | Descriptor: | product of RIKEN cDNA 3110009E22 | | Authors: | Suzuki, S, Hatanaka, H, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-07-10 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the retroviral Gag MA-like domain of RIKEN cDNA 3110009E22
To be Published
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5Y4G
 | | Apo Structure of AmbP3 | | Descriptor: | AmbP3 | | Authors: | Wong, C.P, Awakawa, T, Nakashima, Y. | | Deposit date: | 2017-08-03 | | Release date: | 2018-07-18 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Angew. Chem. Int. Ed. Engl., 57, 2018
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7DE4
 | | Hybrid cluster protein (HCP) from Escherichia coli | | Descriptor: | FE-S-O HYBRID CLUSTER, Hydroxylamine reductase, IRON/SULFUR CLUSTER | | Authors: | Fujishiro, T, Ooi, M, Takaoka, K, Takahashi, Y. | | Deposit date: | 2020-11-02 | | Release date: | 2021-06-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.61 Å) | | Cite: | Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion.
Febs J., 288, 2021
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5Y72
 | | DMSPP Bound AmbP3 | | Descriptor: | AmbP3, DIMETHYLALLYL S-THIOLODIPHOSPHATE | | Authors: | Wong, C.P, Awakawa, T, Nakashima, Y. | | Deposit date: | 2017-08-16 | | Release date: | 2018-07-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Angew. Chem. Int. Ed. Engl., 57, 2018
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5Y84
 | | Hapalindole U and DMSPP Bound AmbP3 | | Descriptor: | AmbP3, DIMETHYLALLYL S-THIOLODIPHOSPHATE, Hapalindole U | | Authors: | Wong, C.P, Awakawa, T, Nakashima, Y. | | Deposit date: | 2017-08-18 | | Release date: | 2018-07-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Angew. Chem. Int. Ed. Engl., 57, 2018
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5Y7C
 | | Hapalindole A and DMSPP Bound AmbP3 | | Descriptor: | AmbP3, DIMETHYLALLYL S-THIOLODIPHOSPHATE, Hapalindole A | | Authors: | Wong, C.P, Awakawa, T, Nakashima, Y. | | Deposit date: | 2017-08-16 | | Release date: | 2018-07-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.003 Å) | | Cite: | Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3
Angew. Chem. Int. Ed. Engl., 57, 2018
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2ZBZ
 | | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D3 | | Descriptor: | 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL, Cytochrome P450-SU1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Sugimoto, H, Shinkyo, R, Hayashi, K, Yoneda, S, Yamada, M, Kamakura, M, Ikushiro, S, Shiro, Y, Sakaki, T. | | Deposit date: | 2007-10-30 | | Release date: | 2008-04-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structure of CYP105A1 (P450SU-1) in Complex with 1alpha,25-Dihydroxyvitamin D3
Biochemistry, 47, 2008
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2ZV2
 | | Crystal structure of human calcium/calmodulin-dependent protein kinase kinase 2, beta, CaMKK2 kinase domain in complex with STO-609 | | Descriptor: | 7-oxo-7H-benzimidazo[2,1-a]benz[de]isoquinoline-3-carboxylic acid, Calcium/calmodulin-dependent protein kinase kinase 2 | | Authors: | Yoshikawa, S, Kukimoto-niino, M, Shirouzu, M, Suzuki, A, Lee, S, Minokoshi, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-10-31 | | Release date: | 2009-11-03 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of the Ca2+/calmodulin-dependent protein kinase kinase in complex with the inhibitor STO-609
J.Biol.Chem., 286, 2011
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