8IPB
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![BU of 8ipb by Molmil](/molmil-images/mine/8ipb) | Wheat 80S ribosome pausing on AUG-Stop with cycloheximide | Descriptor: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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2DPC
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![BU of 2dpc by Molmil](/molmil-images/mine/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
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![BU of 2dp7 by Molmil](/molmil-images/mine/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
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![BU of 2dpb by Molmil](/molmil-images/mine/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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2DQQ
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![BU of 2dqq by Molmil](/molmil-images/mine/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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2DQP
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![BU of 2dqp by Molmil](/molmil-images/mine/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
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![BU of 2dqo by Molmil](/molmil-images/mine/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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5XOD
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![BU of 5xod by Molmil](/molmil-images/mine/5xod) | Crystal structure of human Smad2-Ski complex | Descriptor: | Mothers against decapentaplegic homolog 2, Ski oncogene | Authors: | Miyazono, K, Moriwaki, S, Ito, T, Tanokura, M. | Deposit date: | 2017-05-27 | Release date: | 2018-03-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.851 Å) | Cite: | Hydrophobic patches on SMAD2 and SMAD3 determine selective binding to cofactors Sci Signal, 11, 2018
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4WRI
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![BU of 4wri by Molmil](/molmil-images/mine/4wri) | Crystal structure of okadaic acid binding protein 2.1 | Descriptor: | OKADAIC ACID, Okadaic acid binding protein 2-alpha | Authors: | Ehara, H, Makino, M, Kodama, K, Ito, T, Sekine, S, Fukuzawa, S, Yokoyama, S, Tachibana, K. | Deposit date: | 2014-10-24 | Release date: | 2015-05-27 | Last modified: | 2020-02-05 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation Chembiochem, 16, 2015
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5AWJ
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![BU of 5awj by Molmil](/molmil-images/mine/5awj) | Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor,Vitamin D3 receptor | Authors: | Anami, Y, Itoh, T, Inaba, Y, Nakabayashi, M, Ikura, T, Ito, N, Yamamoto, K. | Deposit date: | 2015-07-04 | Release date: | 2015-11-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity. Bioorg.Med.Chem., 23, 2015
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5B04
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![BU of 5b04 by Molmil](/molmil-images/mine/5b04) | Crystal structure of the eukaryotic translation initiation factor 2B from Schizosaccharomyces pombe | Descriptor: | PHOSPHATE ION, Probable translation initiation factor eIF-2B subunit beta, Probable translation initiation factor eIF-2B subunit delta, ... | Authors: | Kashiwagi, K, Ito, T, Yokoyama, S. | Deposit date: | 2015-10-27 | Release date: | 2016-02-24 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.994 Å) | Cite: | Crystal structure of eukaryotic translation initiation factor 2B Nature, 531, 2016
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5B19
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![BU of 5b19 by Molmil](/molmil-images/mine/5b19) | Picrophilus torridus aspartate racemase | Descriptor: | Aspartate racemase, L(+)-TARTARIC ACID | Authors: | Aihara, T, Ito, T, Yamanaka, Y, Noguchi, K, Odaka, M, Sekine, M, Homma, H, Yohda, M. | Deposit date: | 2015-11-30 | Release date: | 2016-06-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.851 Å) | Cite: | Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus Extremophiles, 20, 2016
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7CPJ
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![BU of 7cpj by Molmil](/molmil-images/mine/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: | 2024-05-29 | 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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6L2N
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![BU of 6l2n by Molmil](/molmil-images/mine/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
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![BU of 6l2o by Molmil](/molmil-images/mine/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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7D45
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![BU of 7d45 by Molmil](/molmil-images/mine/7d45) | eIF2B-eIF2(aP), aP1 complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2021-01-27 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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7D44
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![BU of 7d44 by Molmil](/molmil-images/mine/7d44) | eIF2B-eIF2(aP), aP2 complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2021-01-27 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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7D46
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![BU of 7d46 by Molmil](/molmil-images/mine/7d46) | eIF2B apo | Descriptor: | Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, Translation initiation factor eIF-2B subunit delta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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7D43
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![BU of 7d43 by Molmil](/molmil-images/mine/7d43) | eIF2B-eIF2(aP), aPg complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Eukaryotic translation initiation factor 2 subunit 2, Eukaryotic translation initiation factor 2 subunit 3, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2021-01-27 | Method: | ELECTRON MICROSCOPY (4.3 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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6M64
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![BU of 6m64 by Molmil](/molmil-images/mine/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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6M3L
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![BU of 6m3l by Molmil](/molmil-images/mine/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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8IP8
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![BU of 8ip8 by Molmil](/molmil-images/mine/8ip8) | Wheat 80S ribosome stalled on AUG-Stop boron dependently | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein eL8, 40S ribosomal protein eS1, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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5ZC9
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![BU of 5zc9 by Molmil](/molmil-images/mine/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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5YE4
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![BU of 5ye4 by Molmil](/molmil-images/mine/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
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![BU of 5ye3 by Molmil](/molmil-images/mine/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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