2Z0A
| Crystal structure of RNA-binding domain of NS1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1) | Descriptor: | GLYCINE, Nonstructural protein 1, SUCCINIC ACID | Authors: | Saijo, S, Kishishita, S, Kamo-Uchikubo, T, Terada, T, Shirouzu, M, Ito, H, Ito, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-05-07 | Release date: | 2008-05-13 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structure of RNA-binding domain of NS1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1) To be Published
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2Z16
| Crystal structure of Matrix protein 1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1) | Descriptor: | Matrix protein 1 | Authors: | Saijo, S, Kishishita, S, Uchikubo-Kamo, T, Terada, T, Shirouzu, M, Ito, H, Ito, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-05-08 | Release date: | 2008-05-13 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.02 Å) | Cite: | Crystal structure of Matrix protein 1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1) To be Published
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6L2N
| Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) complex | Descriptor: | DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3'), RE_R_Pab1 domain-containing protein | Authors: | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | Deposit date: | 2019-10-05 | Release date: | 2020-03-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI. Nucleic Acids Res., 48, 2020
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6L2O
| Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex | Descriptor: | DNA (5'-D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-3'), RE_R_Pab1 domain-containing protein | Authors: | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | Deposit date: | 2019-10-05 | Release date: | 2020-03-18 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI. Nucleic Acids Res., 48, 2020
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6M3L
| Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex | Descriptor: | DNA (5'-D(*CP*GP*CP*AP*TP*CP*GP*AP*TP*TP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*GP*CP*G)-3'), RE_R_Pab1 domain-containing protein | Authors: | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | Deposit date: | 2020-03-04 | Release date: | 2020-03-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI. Nucleic Acids Res., 48, 2020
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6M64
| Crystal structure of SMAD2 in complex with CBP | Descriptor: | CBP, Mothers against decapentaplegic homolog 2 | Authors: | Miyazono, K, Ito, T, Wada, H, Tanokura, M. | Deposit date: | 2020-03-13 | Release date: | 2020-11-25 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structural basis for transcriptional coactivator recognition by SMAD2 in TGF-beta signaling. Sci.Signal., 13, 2020
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5YE4
| Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | Descriptor: | 1A9D7 L chain, 1A9D7 VH CH1 chain, ZINC ION, ... | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | Deposit date: | 2017-09-15 | Release date: | 2018-08-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.799 Å) | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics, 13, 2018
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5YE3
| Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment | Descriptor: | 2A7D9 L chain, 2A7D9 VH CH1 chain, di-acetylated histone H4 | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | Deposit date: | 2017-09-15 | Release date: | 2018-08-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics, 13, 2018
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7CFA
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7CO1
| Crystal structure of SMAD2 in complex with wild-type CBP | Descriptor: | CREB-binding protein, Mothers against decapentaplegic homolog 2 | Authors: | Miyazono, K, Wada, H, Ito, T, Tanokura, M. | Deposit date: | 2020-08-03 | Release date: | 2020-11-25 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Structural basis for transcriptional coactivator recognition by SMAD2 in TGF-beta signaling. Sci.Signal., 13, 2020
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5XWD
| Crystal structure of the complex of 059-152-Fv and EGFR-ECD | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Epidermal growth factor receptor, ... | Authors: | Matsuda, T, Ito, T, Shirouzu, M. | Deposit date: | 2017-06-29 | Release date: | 2018-02-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.894 Å) | Cite: | Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction PLoS ONE, 13, 2018
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2DPC
| Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, COBALT (II) ION, DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*(OMU)P*DCP*DGP*DCP*DG)-3'), ... | Authors: | Juan, E.C.M, Kondo, J, Kurihara, T, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-08 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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2DP7
| Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3'), MAGNESIUM ION, ... | Authors: | Juan, E.C.M, Kondo, J, Kurihara, T, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-08 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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2DPB
| Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3'), POTASSIUM ION | Authors: | Juan, E.C.M, Kondo, J, Kurihara, T, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-08 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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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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3VSS
| Microbacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain complexed with fructose | Descriptor: | Beta-fructofuranosidase, beta-D-fructofuranose | Authors: | Tonozuka, T, Tamaki, A, Yokoi, G, Miyazaki, T, Ichikawa, M, Nishikawa, A, Ohta, Y, Hidaka, Y, Katayama, K, Hatada, Y, Ito, T, Fujita, K. | Deposit date: | 2012-05-08 | Release date: | 2012-08-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.97 Å) | Cite: | Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 beta-fructofuranosidase Enzyme.Microb.Technol., 51, 2012
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3VSR
| Microbacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain | Descriptor: | Beta-fructofuranosidase | Authors: | Tonozuka, T, Tamaki, A, Yokoi, G, Miyazaki, T, Ichikawa, M, Nishikawa, A, Ohta, Y, Hidaka, Y, Katayama, K, Hatada, Y, Ito, T, Fujita, K. | Deposit date: | 2012-05-08 | Release date: | 2012-08-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 beta-fructofuranosidase Enzyme.Microb.Technol., 51, 2012
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5ZC9
| Crystal structure of the human eIF4A1-ATP analog-RocA-polypurine RNA complex | Descriptor: | (1R,2R,3S,3aR,8bS)-6,8-dimethoxy-3a-(4-methoxyphenyl)-N,N-dimethyl-1,8b-bis(oxidanyl)-3-phenyl-2,3-dihydro-1H-cyclopenta[b][1]benzofuran-2-carboxamide, Eukaryotic initiation factor 4A-I, MAGNESIUM ION, ... | Authors: | Iwasaki, W, Takahashi, M, Sakamoto, A, Iwasaki, S, Ito, T. | Deposit date: | 2018-02-16 | Release date: | 2019-01-16 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Mol. Cell, 73, 2019
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3WX1
| Mouse Cereblon thalidomide binding domain, selenomethionine derivative | Descriptor: | Protein cereblon, SULFATE ION, ZINC ION | Authors: | Mori, T, Ito, T, Hirano, Y, Yamaguchi, Y, Handa, H, Hakoshima, T. | Deposit date: | 2014-07-10 | Release date: | 2014-08-06 | Last modified: | 2014-09-17 | Method: | X-RAY DIFFRACTION (1.93 Å) | Cite: | Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs Nat.Struct.Mol.Biol., 21, 2014
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3WX2
| Mouse Cereblon thalidomide binding domain, native | Descriptor: | Protein cereblon, SULFATE ION, ZINC ION | Authors: | Mori, T, Ito, T, Hirano, Y, Yamaguchi, Y, Handa, H, Hakoshima, T. | Deposit date: | 2014-07-10 | Release date: | 2014-08-06 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs Nat.Struct.Mol.Biol., 21, 2014
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2DQQ
| Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') | Authors: | Juan, E.C.M, Kondo, J, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-29 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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7F5S
| human delta-METTL18 60S ribosome | Descriptor: | 28S rRNA, 5.8S rRNA, 5S rRNA, ... | Authors: | Takahashi, M, Kashiwagi, K, Ito, T. | Deposit date: | 2021-06-22 | Release date: | 2022-06-22 | Method: | ELECTRON MICROSCOPY (2.72 Å) | Cite: | METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance. Elife, 11, 2022
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2DQP
| Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') | Authors: | Juan, E.C.M, Kondo, J, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-29 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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2DQO
| Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine | Descriptor: | (6-AMINOHEXYL)CARBAMIC ACID, BARIUM ION, DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3'), ... | Authors: | Juan, E.C.M, Kondo, J, Ito, T, Ueno, Y, Matsuda, A, Takenaka, A. | Deposit date: | 2006-05-29 | Release date: | 2007-04-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Nucleic Acids Res., 35, 2007
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3A98
| Crystal structure of the complex of the interacting regions of DOCK2 and ELMO1 | Descriptor: | Dedicator of cytokinesis protein 2, Engulfment and cell motility protein 1 | Authors: | Hanawa-Suetsugu, K, Kukimoto-Niino, M, Sekine, S, Ito, T, Mishima-Tsumagari, C, Terada, T, Shirouzu, M, Fukui, Y, Yokoyama, S. | Deposit date: | 2009-10-21 | Release date: | 2010-10-27 | Last modified: | 2019-09-04 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms. Proc.Natl.Acad.Sci.USA, 109, 2012
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