4GTX
 
 | | Crystal structure of mouse Enpp1 in complex with TMP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Kato, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2012-08-29 | | Release date: | 2012-11-07 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (3.201 Å) | | Cite: | Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Proc.Natl.Acad.Sci.USA, 109, 2012
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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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4IKX
 | | Crystal structure of peptide transporter POT (E310Q mutant) | | Descriptor: | Di-tripeptide ABC transporter (Permease), OLEIC ACID, SULFATE ION | | Authors: | Doki, S, Kato, H.E, Ishitani, R, Nureki, O. | | Deposit date: | 2012-12-28 | | Release date: | 2013-07-10 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT.
Proc.Natl.Acad.Sci.USA, 110, 2013
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3G5Q
 | | Crystal structure of Thermus thermophilus TrmFO | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, FLAVIN-ADENINE DINUCLEOTIDE, Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO | | Authors: | Nishimasu, H, Ishitani, R, Hori, H, Nureki, O. | | Deposit date: | 2009-02-05 | | Release date: | 2009-05-19 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.102 Å) | | Cite: | Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Proc.Natl.Acad.Sci.USA, 106, 2009
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4IKV
 | | Crystal structure of peptide transporter POT | | Descriptor: | (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Di-tripeptide ABC transporter (Permease), OLEIC ACID, ... | | Authors: | Doki, S, Kato, H.E, Ishitani, R, Nureki, O. | | Deposit date: | 2012-12-28 | | Release date: | 2013-07-10 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT.
Proc.Natl.Acad.Sci.USA, 110, 2013
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3G5S
 | | Crystal structure of Thermus thermophilus TrmFO in complex with glutathione | | Descriptor: | 1,2-ETHANEDIOL, FLAVIN-ADENINE DINUCLEOTIDE, GLUTATHIONE, ... | | Authors: | Nishimasu, H, Ishitani, R, Hori, H, Nureki, O. | | Deposit date: | 2009-02-05 | | Release date: | 2009-05-19 | | Last modified: | 2025-03-26 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Proc.Natl.Acad.Sci.USA, 106, 2009
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3VU8
 | | Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue | | Descriptor: | Methionine--tRNA ligase, N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE, ZINC ION | | Authors: | Konno, M, Kato-Murayama, M, Toma-Fukai, S, Uchikawa, E, Nureki, O, Yokoyama, S. | | Deposit date: | 2012-06-22 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases
To be Published
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4KPP
 | | Crystal Structure of H+/Ca2+ Exchanger CAX | | Descriptor: | (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, CALCIUM ION, OLEIC ACID, ... | | Authors: | Nishizawa, T, Ishitani, R, Nureki, O. | | Deposit date: | 2013-05-14 | | Release date: | 2013-06-26 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger.
Science, 341, 2013
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4L3O
 | | Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 | | Descriptor: | 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, NAD-dependent protein deacetylase sirtuin-2, ... | | Authors: | Yamagata, K, Nishimasu, H, Ishitani, R, Nureki, O. | | Deposit date: | 2013-06-06 | | Release date: | 2014-02-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.518 Å) | | Cite: | Structural Basis for Potent Inhibition of SIRT2 Deacetylase by a Macrocyclic Peptide Inducing Dynamic Structural Change
Structure, 22, 2013
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5Y78
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with inorganic phosphate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, PHOSPHATE ION, Putative hexose phosphate translocator | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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5Y79
 | | Crystal structure of the triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 3-PHOSPHOGLYCERIC ACID, CITRATE ANION, ... | | Authors: | Lee, Y, Nishizawa, T, Takemoto, M, Kumazaki, K, Yamashita, K, Hirata, K, Minoda, A, Nagatoishi, S, Tsumoto, K, Ishitani, R, Nureki, O. | | Deposit date: | 2017-08-16 | | Release date: | 2017-10-04 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structure of the triose-phosphate/phosphate translocator reveals the basis of substrate specificity
Nat Plants, 3, 2017
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6AI6
 | | Crystal structure of SpCas9-NG | | Descriptor: | 1,2-ETHANEDIOL, CRISPR-associated endonuclease Cas9/Csn1, DNA (28-MER), ... | | Authors: | Nishimasu, H, Hirano, S, Ishitani, R, Nureki, O. | | Deposit date: | 2018-08-21 | | Release date: | 2018-10-31 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Engineered CRISPR-Cas9 nuclease with expanded targeting space
Science, 361, 2018
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5ZIH
 | | Crystal structure of the red light-activated channelrhodopsin Chrimson. | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Sensory opsin A,Chrimson | | Authors: | Oda, K, Vierock, J, Oishi, S, Taniguchi, R, Yamashita, K, Nishizawa, T, Hegemann, P, Nureki, O. | | Deposit date: | 2018-03-15 | | Release date: | 2018-11-21 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of the red light-activated channelrhodopsin Chrimson.
Nat Commun, 9, 2018
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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: | 2024-11-13 | | 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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6AEK
 | | Crystal structure of ENPP1 in complex with pApG | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE MONOPHOSPHATE, ... | | Authors: | Kato, K, Nishimasu, H, Hirano, S, Hirano, H, Ishitani, R, Nureki, O. | | Deposit date: | 2018-08-05 | | Release date: | 2019-03-06 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1.
Nat Commun, 9, 2018
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6AEL
 | | Crystal structure of ENPP1 in complex with 3'3'-cGAMP | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one, ... | | Authors: | Kato, K, Nishimasu, H, Hirano, S, Hirano, H, Ishitani, R, Nureki, O. | | Deposit date: | 2018-08-05 | | Release date: | 2019-03-06 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1.
Nat Commun, 9, 2018
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8IY6
 | | ETB-Gi complex bound to Endotheline-1, focused on receptor | | Descriptor: | Endothelin type B receptor, Endothelin-1 | | Authors: | Sano, F.K, Akasaka, H, Shihoya, W, Nureki, O. | | Deposit date: | 2023-04-04 | | Release date: | 2023-08-16 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (3.13 Å) | | Cite: | Cryo-EM structure of the endothelin-1-ET B -G i complex.
Elife, 12, 2023
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8IY5
 | | ETB-Gi complex bound to endothelin-1 | | Descriptor: | Endothelin type B receptor, Endothelin-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ... | | Authors: | Sano, F.K, Akasaka, H, Shihoya, W, Nureki, O. | | Deposit date: | 2023-04-04 | | Release date: | 2023-08-16 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Cryo-EM structure of the endothelin-1-ET B -G i complex.
Elife, 12, 2023
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8J12
 | | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (247-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-12 | | Release date: | 2023-09-27 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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8J1J
 | | Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (118-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-13 | | Release date: | 2023-09-27 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (2.91 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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8J3R
 | | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-18 | | Release date: | 2023-09-27 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (2.95 Å) | | Cite: | An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.
Cell, 186, 2023
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5GVS
 | | Crystal structure of the DDX41 DEAD domain in an apo open form | | Descriptor: | Probable ATP-dependent RNA helicase DDX41 | | Authors: | Omura, H, Oikawa, D, Nakane, T, Kato, M, Ishii, R, Goto, Y, Suga, H, Ishitani, R, Tokunaga, F, Nureki, O. | | Deposit date: | 2016-09-06 | | Release date: | 2016-10-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide
Sci Rep, 6, 2016
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8J97
 | | Structure of Muscarinic receptor (M2R) in complex with beta-arrestin1 (Local refine, cross-linked) | | Descriptor: | Beta-arrestin-1, Fab30 Heavy Chain, Fab30 Light Chain, ... | | Authors: | Maharana, J, Sano, F.K, Shihoya, W, Banerjee, R, Nureki, O, Shukla, A.K. | | Deposit date: | 2023-05-02 | | Release date: | 2023-12-27 | | Last modified: | 2024-10-09 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Molecular insights into atypical modes of beta-arrestin interaction with seven transmembrane receptors.
Science, 383, 2024
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8J8R
 | | Structure of beta-arrestin2 in complex with M2Rpp | | Descriptor: | Beta-arrestin-2, Fab30 Heavy Chain, Fab30 Light Chain, ... | | Authors: | Maharana, J, Sano, F.K, Shihoya, W, Banerjee, R, Nureki, O, Shukla, A.K. | | Deposit date: | 2023-05-02 | | Release date: | 2023-12-27 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Molecular insights into atypical modes of beta-arrestin interaction with seven transmembrane receptors.
Science, 383, 2024
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5GVR
 | | Crystal structure of the DDX41 DEAD domain in an apo closed form | | Descriptor: | (2S)-2-hydroxybutanedioic acid, Probable ATP-dependent RNA helicase DDX41 | | Authors: | Omura, H, Oikawa, D, Nakane, T, Kato, M, Ishii, R, Goto, Y, Suga, H, Ishitani, R, Tokunaga, F, Nureki, O. | | Deposit date: | 2016-09-06 | | Release date: | 2016-10-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide
Sci Rep, 6, 2016
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