7Y7D
| Structure of the Bacterial Ribosome with human tRNA Asp(Q34) and mRNA(GAU) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.58 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7Y7G
| Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.34 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7Y7C
| Structure of the Bacterial Ribosome with human tRNA Asp(G34) and mRNA(GAU) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.51 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7Y7F
| Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAC) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.43 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7Y7E
| Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.41 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7Y7H
| Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAC) | Descriptor: | 16S rRNA, 23S rRNA, 30S ribosomal protein S10, ... | Authors: | Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T. | Deposit date: | 2022-06-22 | Release date: | 2023-10-25 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.51 Å) | Cite: | Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell, 186, 2023
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7EQE
| Crystal Structure of a transcription factor | Descriptor: | TetR/AcrR family transcriptional regulator | Authors: | Uehara, S, Tsugita, A, Matsui, T, Yokoyama, T, Ostash, I, Ostash, B, Tanaka, Y. | Deposit date: | 2021-05-01 | Release date: | 2022-04-27 | Last modified: | 2022-10-19 | Method: | X-RAY DIFFRACTION (2.399 Å) | Cite: | The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK. Febs J., 289, 2022
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7EQF
| Crystal Structure of a Transcription Factor in complex with Ligand | Descriptor: | (6~{R})-3-methyl-8-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{R},5~{R},6~{R})-6-methyl-4-[(2~{S},5~{S},6~{S})-6-methyl-5-[(2~{S},4~{R},5~{S},6~{R})-6-methyl-5-[(2~{S},4~{S},5~{S},6~{R})-6-methyl-4-[(2~{S},5~{S},6~{S})-6-methyl-5-oxidanyl-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-oxan-2-yl]oxy-5-oxidanyl-oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-1,6,11-tris(oxidanyl)-5,6-dihydrobenzo[a]anthracene-7,12-dione, TetR/AcrR family transcriptional regulator | Authors: | Uehara, S, Tsugita, A, Matsui, T, Yokoyama, T, Ostash, I, Ostash, B, Tanaka, Y. | Deposit date: | 2021-05-01 | Release date: | 2022-04-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.91 Å) | Cite: | The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK. Febs J., 289, 2022
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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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8HSP
| E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 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: | 2022-12-20 | Release date: | 2024-04-03 | Last modified: | 2024-04-10 | Method: | ELECTRON MICROSCOPY (2.32 Å) | Cite: | Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Nat.Struct.Mol.Biol., 2024
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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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5HNY
| Structural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the AMPPNP state | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shigematsu, H, Yokoyama, T, Kikkawa, M, Shirouzu, M, Nitta, R. | Deposit date: | 2016-01-19 | Release date: | 2016-08-10 | Last modified: | 2016-11-02 | Method: | ELECTRON MICROSCOPY (6.3 Å) | Cite: | Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility Structure, 24, 2016
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5HNZ
| Structural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the nucleotide-free state | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shigematsu, H, Yokoyama, T, Kikkawa, M, Shirouzu, M, Nitta, R. | Deposit date: | 2016-01-19 | Release date: | 2016-08-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (5.8 Å) | Cite: | Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility Structure, 24, 2016
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5HNX
| Structural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the nucleotide-free state | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shigematsu, H, Yokoyama, T, Kikkawa, M, Shirouzu, M, Nitta, R. | Deposit date: | 2016-01-19 | Release date: | 2016-08-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (6.6 Å) | Cite: | Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility Structure, 24, 2016
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5HNW
| Structural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the AMPPNP state | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Shigematsu, H, Yokoyama, T, Kikkawa, M, Shirouzu, M, Nitta, R. | Deposit date: | 2016-01-19 | Release date: | 2016-08-10 | Last modified: | 2018-07-25 | Method: | ELECTRON MICROSCOPY (6.6 Å) | Cite: | Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility Structure, 24, 2016
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6M04
| Structure of the human homo-hexameric LRRC8D channel at 4.36 Angstroms | Descriptor: | Volume-regulated anion channel subunit LRRC8D | Authors: | Nakamura, R, Kasuya, G, Yokoyama, T, Shirouzu, M, Ishitani, R, Nureki, O. | Deposit date: | 2020-02-20 | Release date: | 2020-06-17 | Method: | ELECTRON MICROSCOPY (4.36 Å) | Cite: | Cryo-EM structure of the volume-regulated anion channel LRRC8D isoform identifies features important for substrate permeation. Commun Biol, 3, 2020
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6JMR
| CD98hc extracellular domain bound to HBJ127 Fab and MEM-108 Fab | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 4F2 cell-surface antigen heavy chain, ... | Authors: | Lee, Y, Nishizawa, T, Kusakizako, T, Oda, K, Ishitani, R, Yokoyama, T, Nakane, T, Shirouzu, M, Nureki, O. | Deposit date: | 2019-03-13 | Release date: | 2019-06-19 | Last modified: | 2020-07-29 | Method: | ELECTRON MICROSCOPY (4.1 Å) | Cite: | Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc. Nat.Struct.Mol.Biol., 26, 2019
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5ZSU
| Structure of the human homo-hexameric LRRC8A channel at 4.25 Angstroms | Descriptor: | Volume-regulated anion channel subunit LRRC8A | Authors: | Kasuya, G, Nakane, T, Yokoyama, T, Shirouzu, M, Ishitani, R, Nureki, O. | Deposit date: | 2018-04-29 | Release date: | 2018-08-15 | Last modified: | 2018-09-26 | Method: | ELECTRON MICROSCOPY (4.25 Å) | Cite: | Cryo-EM structures of the human volume-regulated anion channel LRRC8. Nat. Struct. Mol. Biol., 25, 2018
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5XON
| RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS | Descriptor: | DNA (48-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | Authors: | Ehara, H, Yokoyama, T, Shigematsu, H, Shirouzu, M, Sekine, S. | Deposit date: | 2017-05-29 | Release date: | 2017-08-16 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.83 Å) | Cite: | Structure of the complete elongation complex of RNA polymerase II with basal factors Science, 357, 2017
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6K72
| eIF2(aP) - eIF2B 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, Yokoyama, T, Ito, T. | Deposit date: | 2019-06-05 | Release date: | 2019-07-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4.6 Å) | Cite: | Structural basis for eIF2B inhibition in integrated stress response. Science, 364, 2019
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6K71
| eIF2 - eIF2B 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, Yokoyama, T, Ito, T. | Deposit date: | 2019-06-05 | Release date: | 2019-07-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4.3 Å) | Cite: | Structural basis for eIF2B inhibition in integrated stress response. Science, 364, 2019
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2EXT
| TRAP4 (engineered TRAP) | Descriptor: | TRYPTOPHAN, Transcription attenuation protein mtrB | Authors: | Heddle, J.G, Yokoyama, T, Yamashita, I, Park, S.Y, Tame, J.R.H. | Deposit date: | 2005-11-08 | Release date: | 2006-08-01 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Rounding up: Engineering 12-Membered Rings from the Cyclic 11-Mer TRAP Structure, 14, 2006
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2DGE
| Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana | Descriptor: | Cytochrome c6, PROTOPORPHYRIN IX CONTAINING FE, ZINC ION | Authors: | Chida, H, Yokoyama, T, Kawai, F, Nakazawa, A, Akazaki, H, Takayama, Y, Hirano, T, Suruga, K, Satoh, T, Yamada, S, Kawachi, R, Unzai, S, Nishio, T, Park, S.-Y, Oku, T. | Deposit date: | 2006-03-11 | Release date: | 2006-07-04 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana Febs Lett., 580, 2006
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2DN1
| 1.25A resolution crystal structure of human hemoglobin in the oxy form | Descriptor: | Hemoglobin alpha subunit, Hemoglobin beta subunit, OXYGEN MOLECULE, ... | Authors: | Park, S.-Y, Yokoyama, T, Shibayama, N, Shiro, Y, Tame, J.R. | Deposit date: | 2006-04-25 | Release date: | 2006-05-09 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | 1.25 a resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J.Mol.Biol., 360, 2006
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2DN3
| 1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form | Descriptor: | CARBON MONOXIDE, Hemoglobin alpha subunit, Hemoglobin beta subunit, ... | Authors: | Park, S.-Y, Yokoyama, T, Shibayama, N, Shiro, Y, Tame, J.R. | Deposit date: | 2006-04-25 | Release date: | 2006-05-09 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | 1.25 a resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. J.Mol.Biol., 360, 2006
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