7CJ3
 
 | | Crystal structure of the transmembrane domain of Salpingoeca rosetta rhodopsin phosphodiesterase | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL | | Authors: | Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O. | | Deposit date: | 2020-07-09 | | Release date: | 2020-11-25 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
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1UFA
 | | Crystal structure of TT1467 from Thermus thermophilus HB8 | | Descriptor: | TT1467 protein | | Authors: | Idaka, M, Terada, T, Murayama, K, Yamaguchi, H, Nureki, O, Ishitani, R, Kuramitsu, S, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-05-28 | | Release date: | 2003-11-28 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of TT1467 from Thermus thermophilus HB8
To be published
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7CCS
 | | Consensus mutated xCT-CD98hc complex | | Descriptor: | 4F2 cell-surface antigen heavy chain, Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System | | Authors: | Oda, K, Lee, Y, Takemoto, M, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-06-17 | | Release date: | 2020-12-09 | | Last modified: | 2024-11-20 | | Method: | ELECTRON MICROSCOPY (6.2 Å) | | Cite: | Consensus mutagenesis approach improves the thermal stability of system x c - transporter, xCT, and enables cryo-EM analyses.
Protein Sci., 29, 2020
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7C7L
 | | Cryo-EM structure of the Cas12f1-sgRNA-target DNA complex | | Descriptor: | CRISPR-associated protein Cas14a.1, DNA (40-mer), ZINC ION, ... | | Authors: | Takeda, N.S, Nakagawa, R, Okazaki, S, Hirano, H, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O. | | Deposit date: | 2020-05-26 | | Release date: | 2020-12-23 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structure of the miniature type V-F CRISPR-Cas effector enzyme.
Mol.Cell, 81, 2021
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7CLJ
 | | Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, RETINAL, SULFATE ION, ... | | Authors: | Tanaka, T, Shihoya, W, Yamashita, K, Nureki, O. | | Deposit date: | 2020-07-21 | | Release date: | 2020-09-02 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for unique color tuning mechanism in heliorhodopsin.
Biochem.Biophys.Res.Commun., 533, 2020
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7C86
 | | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ... | | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-05-28 | | Release date: | 2021-04-07 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
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1ULH
 | | A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase | | Descriptor: | Tryptophanyl-tRNA synthetase | | Authors: | Kise, Y, Sengoku, T, Ishii, R, Yokoyama, S, Park, S.G, Lee, S.W, Kim, S, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-12 | | Release date: | 2004-02-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase
Nat.Struct.Mol.Biol., 11, 2004
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7D7Q
 | | Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL | | Authors: | Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O. | | Deposit date: | 2020-10-05 | | Release date: | 2020-11-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
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1V33
 | | Crystal structure of DNA primase from Pyrococcus horikoshii | | Descriptor: | DNA primase small subunit, PHOSPHATE ION, ZINC ION | | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-25 | | Release date: | 2004-03-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
Genes Cells, 8, 2003
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1V34
 | | Crystal structure of Pyrococcus horikoshii DNA primase-UTP complex | | Descriptor: | DNA primase small subunit, URIDINE 5'-TRIPHOSPHATE, ZINC ION | | Authors: | Ito, N, Nureki, O, Shirouzu, M, Yokoyama, S, Hanaoka, F, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-25 | | Release date: | 2004-03-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
Genes Cells, 8, 2003
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1UDS
 | | Crystal structure of the tRNA processing enzyme RNase PH R126A mutant from Aquifex aeolicus | | Descriptor: | PHOSPHATE ION, Ribonuclease PH, SULFATE ION | | Authors: | Ishii, R, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-05-02 | | Release date: | 2003-09-23 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus
J.Biol.Chem., 278, 2003
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1VFG
 | | Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog | | Descriptor: | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, RNA (75-MER), poly A polymerase | | Authors: | Tomita, K, Fukai, S, Ishitani, R, Ueda, T, Takeuchi, N, Vassylyev, D.G, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-04-13 | | Release date: | 2004-08-10 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for template-independent RNA polymerization.
Nature, 430, 2004
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6IS6
 | | Crystal structure of Thermoplasmatales archaeon heliorhodopsin | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, RETINAL, heliorhodopsin | | Authors: | Shihoya, W, Yamashita, K, Nureki, O. | | Deposit date: | 2018-11-15 | | Release date: | 2019-09-25 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of heliorhodopsin.
Nature, 574, 2019
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1IYW
 | | Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase | | Descriptor: | Valyl-tRNA Synthetase | | Authors: | Fukai, S, Nureki, O, Sekine, S, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-09-10 | | Release date: | 2003-06-17 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
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1IUG
 | | The crystal structure of aspartate aminotransferase which belongs to subgroup IV from Thermus thermophilus | | Descriptor: | PHOSPHATE ION, putative aspartate aminotransferase | | Authors: | Katsura, Y, Shirouzu, M, Yamaguchi, H, Ishitani, R, Nureki, O, Kuramitsu, S, Hayashi, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-03-04 | | Release date: | 2003-11-25 | | Last modified: | 2024-12-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
Proteins, 55, 2004
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7V75
 | | Thermostabilized human prestin in complex with salicylate | | Descriptor: | 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 2-HYDROXYBENZOIC ACID, CHOLESTEROL, ... | | Authors: | Futamata, H, Fukuda, M, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-08-21 | | Release date: | 2022-08-31 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (3.57 Å) | | Cite: | Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility.
Nat Commun, 13, 2022
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2DR8
 | | Complex structure of CCA-adding enzyme with tRNAminiDC and CTP | | Descriptor: | CCA-adding enzyme, CYTIDINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Tomita, K, Ishitani, R, Fukai, S, Nureki, O. | | Deposit date: | 2006-06-08 | | Release date: | 2006-11-14 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Complete crystallographic analysis of the dynamics of CCA sequence addition
Nature, 443, 2006
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7V73
 | | Thermostabilized human prestin in complex with chloride | | Descriptor: | 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, CHLORIDE ION, CHOLESTEROL, ... | | Authors: | Futamata, H, Fukuda, M, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-08-21 | | Release date: | 2022-08-31 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (3.52 Å) | | Cite: | Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility.
Nat Commun, 13, 2022
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1J3E
 | | Crystal Structure of the E.coli SeqA protein complexed with N6-methyladenine- guanine mismatch DNA | | Descriptor: | 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3', 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3', SeqA protein | | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Tanaka, Y, Yamazoe, M, Hiraga, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-01-24 | | Release date: | 2004-05-18 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
Nucleic Acids Res., 32, 2004
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2DER
 | | Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state | | Descriptor: | PHOSPHATE ION, SULFATE ION, tRNA, ... | | Authors: | Numata, T, Ikeuchi, Y, Fukai, S, Suzuki, T, Nureki, O. | | Deposit date: | 2006-02-17 | | Release date: | 2006-08-15 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Snapshots of tRNA sulphuration via an adenylated intermediate
Nature, 442, 2006
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1IQ0
 | | THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE | | Descriptor: | ARGINYL-TRNA SYNTHETASE | | Authors: | Shimada, A, Nureki, O, Goto, M, Takahashi, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-05-24 | | Release date: | 2001-11-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
Proc.Natl.Acad.Sci.USA, 98, 2001
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1J1V
 | | Crystal structure of DnaA domainIV complexed with DnaAbox DNA | | Descriptor: | 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3', 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3', Chromosomal replication initiator protein dnaA | | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Terada, T, Shirouzu, M, Katayama, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-18 | | Release date: | 2003-04-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis of replication origin recognition by the DnaA protein
NUCLEIC ACIDS RES., 31, 2003
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1J2B
 | | Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val) | | Descriptor: | Archaeosine tRNA-guanine transglycosylase, MAGNESIUM ION, ZINC ION, ... | | Authors: | Ishitani, R, Nureki, O, Nameki, N, Okada, N, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-29 | | Release date: | 2003-05-27 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme
Cell(Cambridge,Mass.), 113, 2003
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2DET
 | | Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state | | Descriptor: | SULFATE ION, tRNA, tRNA-specific 2-thiouridylase mnmA | | Authors: | Numata, T, Ikeuchi, Y, Fukai, S, Suzuki, T, Nureki, O. | | Deposit date: | 2006-02-17 | | Release date: | 2006-08-15 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | Snapshots of tRNA sulphuration via an adenylated intermediate
Nature, 442, 2006
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2DRA
 | | Complex structure of CCA-adding enzyme with tRNAminiDCC and ATP | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CCA-adding enzyme, MAGNESIUM ION, ... | | Authors: | Tomita, K, Ishitani, R, Fukai, S, Nureki, O. | | Deposit date: | 2006-06-08 | | Release date: | 2006-11-14 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Complete crystallographic analysis of the dynamics of CCA sequence addition
Nature, 443, 2006
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