8HU1
 
 | | E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and ct6A37 in classical state | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | | Deposit date: | 2022-12-22 | | Release date: | 2024-04-03 | | Last modified: | 2024-04-10 | | Method: | ELECTRON MICROSCOPY (2.69 Å) | | Cite: | Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 2024
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8HTZ
 | | E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state | | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | | Authors: | Akiyama, N, Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | | Deposit date: | 2022-12-22 | | Release date: | 2024-04-03 | | Last modified: | 2024-04-10 | | Method: | ELECTRON MICROSCOPY (2.4 Å) | | Cite: | Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine.
Nat.Struct.Mol.Biol., 2024
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2RS7
 | | Solution structure of the second dsRBD from RNA helicase A | | Descriptor: | ATP-dependent RNA helicase A | | Authors: | Nagata, T, Muto, Y, Tsuda, K, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2011-11-29 | | Release date: | 2012-03-14 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the double-stranded RNA-binding domains from RNA helicase A
Proteins, 80, 2012
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2RS6
 | | Solution structure of the N-terminal dsRBD from RNA helicase A | | Descriptor: | ATP-dependent RNA helicase A | | Authors: | Nagata, T, Muto, Y, Tsuda, K, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2011-11-29 | | Release date: | 2012-03-14 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the double-stranded RNA-binding domains from RNA helicase A
Proteins, 80, 2012
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1UDX
 | | Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, ACETATE ION, the GTP-binding protein Obg | | Authors: | Kukimoto-Niino, M, Shirouzu, M, Murayama, K, Inoue, M, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-05-07 | | Release date: | 2004-03-16 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8.
J.Mol.Biol., 337, 2004
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1UG2
 | | Solution Structure of Mouse Hypothetical Gene (2610100B20Rik) Product Homologous to Myb DNA-binding Domain | | Descriptor: | 2610100B20Rik gene product | | Authors: | Zhao, C, Kigawa, T, Tochio, N, Koshiba, S, Inoue, M, Shirouzu, M, Terada, T, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Tanaka, A, Osanai, T, Arakawa, T, Carninci, P, Kawai, J, Hayashizaki, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-06-11 | | Release date: | 2004-06-22 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of Mouse Hypothetical Gene (2610100B20Rik) Product Homologous to Myb DNA-binding Domain
To be Published
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7CPJ
 | | ycbZ-stalled 70S ribosome | | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Yokoyama, T, Shirouzu, M, Ito, T. | | Deposit date: | 2020-08-07 | | Release date: | 2021-12-08 | | Last modified: | 2023-04-05 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.
Rna, 28, 2022
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7DDQ
 | | Structure of RC-LH1-PufX from Rhodobacter veldkampii | | Descriptor: | 1,2-Distearoyl-sn-glycerophosphoethanolamine, Antenna pigment protein alpha chain, Antenna pigment protein beta chain, ... | | Authors: | Bracun, L, Yamagata, A, Shirouzu, M, Liu, L.N. | | Deposit date: | 2020-10-29 | | Release date: | 2021-06-30 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.84 Å) | | Cite: | Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution.
Sci Adv, 7, 2021
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3UG2
 | | Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with gefitinib | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Epidermal growth factor receptor, Gefitinib | | Authors: | Parker, L.J, Handa, N, Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2011-11-02 | | Release date: | 2012-03-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 32, 2013
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3UG1
 | | Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in the apo form | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Epidermal growth factor receptor | | Authors: | Parker, L.J, Handa, N, Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2011-11-02 | | Release date: | 2012-03-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
Oncogene, 32, 2013
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7EG2
 | | Crystal structure of the apoAequorin complex with (S)-daCTZ | | Descriptor: | (2~{S})-2-(hydroxymethyl)-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-3~{H}-inden-1-one, Aequorin-2 | | Authors: | Tomabechi, Y, Shirouzu, M. | | Deposit date: | 2021-03-24 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.22 Å) | | Cite: | Chiral deaza-coelenterazine analogs for probing a substrate-binding site in the Ca2+-binding photoprotein aequorin.
Plos One, 16, 2021
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7EG3
 | | Crystal structure of the apoAequorin complex with (S)-HM-daCTZ | | Descriptor: | (2~{S})-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-2,3-dihydroinden-1-one, Aequorin-2 | | Authors: | Tomabechi, Y, Shirouzu, M. | | Deposit date: | 2021-03-24 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Chiral deaza-coelenterazine analogs for probing a substrate-binding site in the Ca2+-binding photoprotein aequorin.
Plos One, 16, 2021
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3VJN
 | | Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with AMPPNP. | | Descriptor: | Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Semba, K, Yamamoto, T, Yokoyama, S. | | Deposit date: | 2011-10-27 | | Release date: | 2012-03-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene, 32, 2013
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3VA2
 | | Crystal structure of human Interleukin-5 in complex with its alpha receptor | | Descriptor: | Interleukin-5, Interleukin-5 receptor subunit alpha | | Authors: | Kusano, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2011-12-28 | | Release date: | 2012-07-25 | | Method: | X-RAY DIFFRACTION (2.703 Å) | | Cite: | Structural basis of interleukin-5 dimer recognition by its alpha receptor
Protein Sci., 21, 2012
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3VHL
 | | Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant) | | Descriptor: | Cell division control protein 42 homolog, Dedicator of cytokinesis protein 8, PHOSPHATE ION | | Authors: | Hanawa-Suetsugu, K, Kukimoto-Niino, M, Nishizak, T, Terada, T, Shirouzu, M, Fukui, Y, Yokoyama, S. | | Deposit date: | 2011-08-26 | | Release date: | 2012-06-20 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.085 Å) | | Cite: | DOCK8 is a Cdc42 activator critical for interstitial dendritic cell migration during immune responses.
Blood, 119, 2012
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3VJO
 | | Crystal structure of the wild-type EGFR kinase domain in complex with AMPPNP. | | Descriptor: | Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Semba, K, Yamamoto, T, Yokoyama, S. | | Deposit date: | 2011-10-27 | | Release date: | 2012-03-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene, 32, 2013
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3WEX
 | | Crystal structure of HLA-DP5 in complex with Cry j 1-derived peptide (residues 214-222) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MHC class II antigen | | Authors: | Kusano, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-07-16 | | Release date: | 2014-07-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for the specific recognition of the major antigenic peptide from the Japanese cedar pollen allergen Cry j 1 by HLA-DP5
J. Mol. Biol., 426, 2014
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3WU6
 | | Oxidized E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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3WU5
 | | Reduced E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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3WU3
 | | Reduced-form structure of E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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7X73
 | | Structure of G9a in complex with RK-701 | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Histone-lysine N-methyltransferase EHMT2, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-03-09 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.49 Å) | | Cite: | A specific G9a inhibitor unveils BGLT3 lncRNA as a universal mediator of chemically induced fetal globin gene expression.
Nat Commun, 14, 2023
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7X9U
 | | Type-II KH motif of human mitochondrial RbfA | | Descriptor: | Putative ribosome-binding factor A, mitochondrial | | Authors: | Kuwasako, K, Suzuki, S, Furue, M, Takizawa, M, Takahashi, M, Tsuda, K, Nagata, T, Watanabe, S, Tanaka, A, Kobayashi, N, Kigawa, T, Guntert, P, Shirouzu, M, Yokoyama, S, Muto, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2022-03-16 | | Release date: | 2023-01-25 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | 1 H, 13 C, and 15 N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis.
Biomol.Nmr Assign., 16, 2022
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3WU4
 | | Oxidized-form structure of E.coli Lon Proteolytic domain | | Descriptor: | Lon protease, SULFATE ION | | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | | Deposit date: | 2014-04-22 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Nat. Chem. Biol., 11, 2015
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7Y4A
 | | Crystal structure of human ELMO1 RBD-RhoG complex | | Descriptor: | Engulfment and cell motility protein 1, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Tsuda, K, Kukimoto-Niino, M, Shirouzu, M. | | Deposit date: | 2022-06-14 | | Release date: | 2023-03-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Targeting Ras-binding domain of ELMO1 by computational nanobody design.
Commun Biol, 6, 2023
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1UHF
 | | Solution Structure of the third SH3 domain of human intersectin 2(KIAA1256) | | Descriptor: | INTERSECTIN 2 | | Authors: | Suzuki, S, Hatanaka, H, Koshiba, S, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-07-03 | | Release date: | 2004-08-10 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of the third SH3 domain of human intersectin 2(KIAA1256)
To be Published
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