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
| 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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4YVH
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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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4YOW
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4YOX
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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
| 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
| 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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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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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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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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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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8IPA
| Wheat 80S ribosome stalled on AUG-Stop boron dependently 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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8IP9
| Wheat 40S ribosome in complex with a tRNAi | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein S23, 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 (3 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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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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2MGZ
| Solution structure of RBFOX family ASD-1 RRM and SUP-12 RRM in ternary complex with RNA | Descriptor: | Protein ASD-1, isoform a, Protein SUP-12, ... | Authors: | Takahashi, M, Kuwasako, K, Unzai, S, Tsuda, K, Yoshikawa, S, He, F, Kobayashi, N, Guntert, P, Shirouzu, M, Ito, T, Tanaka, A, Yokoyama, S, Hagiwara, M, Kuroyanagi, H, Muto, Y. | Deposit date: | 2013-11-12 | Release date: | 2014-08-13 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing Nat.Struct.Mol.Biol., 21, 2014
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2ZZN
| The complex structure of aTrm5 and tRNACys | Descriptor: | MAGNESIUM ION, RNA (71-MER), S-ADENOSYLMETHIONINE, ... | Authors: | Goto-Ito, S, Ito, T, Yokoyama, S. | Deposit date: | 2009-02-19 | Release date: | 2009-09-15 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat.Struct.Mol.Biol., 16, 2009
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2ZZM
| The complex structure of aTrm5 and tRNALeu | Descriptor: | MAGNESIUM ION, RNA (84-MER), S-ADENOSYLMETHIONINE, ... | Authors: | Goto-Ito, S, Ito, T, Yokoyama, S. | Deposit date: | 2009-02-19 | Release date: | 2009-09-15 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation Nat.Struct.Mol.Biol., 16, 2009
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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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2YX0
| Crystal structure of P. horikoshii TYW1 | Descriptor: | radical sam enzyme | Authors: | Goto-Ito, S, Ishii, R, Ito, T, Shibata, R, Fusatomi, E, Sekine, S, Bessho, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-04-23 | Release date: | 2007-10-30 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.21 Å) | Cite: | Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis Acta Crystallogr.,Sect.D, 63, 2007
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2YX1
| Crystal structure of M.jannaschii tRNA m1G37 methyltransferase | Descriptor: | Hypothetical protein MJ0883, SINEFUNGIN, ZINC ION | Authors: | Goto-Ito, S, Ito, T, Ishii, R, Bessho, Y, Yokoyama, S. | Deposit date: | 2007-04-23 | Release date: | 2008-04-22 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins, 72, 2008
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3AXZ
| Crystal structure of Haemophilus influenzae TrmD in complex with adenosine | Descriptor: | ADENOSINE, tRNA (guanine-N(1)-)-methyltransferase | Authors: | Yoshida, K, Goto-Ito, S, Ito, T, Hou, Y.M, Yokoyama, S. | Deposit date: | 2011-04-21 | Release date: | 2011-08-17 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. Rna, 17, 2011
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