7E6Y
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond 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, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | 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: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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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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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: | 2023-11-22 | 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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3S7T
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5X2G
| Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM) | Descriptor: | 1,2-ETHANEDIOL, CRISPR-associated endonuclease Cas9, Non-target DNA strand, ... | Authors: | Yamada, M, Watanabe, Y, Hirano, H, Nakane, T, Ishitani, R, Nishimasu, H, Nureki, O. | Deposit date: | 2017-01-31 | Release date: | 2017-03-29 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems Mol. Cell, 65, 2017
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5X2H
| Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACA PAM) | Descriptor: | 1,2-ETHANEDIOL, CRISPR-associated endonuclease Cas9, Non-target DNA strand, ... | Authors: | Yamada, M, Watanabe, Y, Hirano, H, Nakane, T, Ishitani, R, Nishimasu, H, Nureki, O. | Deposit date: | 2017-01-31 | Release date: | 2017-03-29 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems Mol. Cell, 65, 2017
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4PDN
| Crystal structure of E. coli YfcM | Descriptor: | MAGNESIUM ION, Uncharacterized protein | Authors: | Kobayashi, K, Ishii, R, Ishitani, R, Nureki, O. | Deposit date: | 2014-04-19 | Release date: | 2015-03-04 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.448 Å) | Cite: | The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation. Nucleic Acids Res., 42, 2014
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4MKP
| Crystal structure of human cGAS apo form | Descriptor: | Cyclic GMP-AMP synthase, ZINC ION | Authors: | Kato, K, Ishii, R, Ishitani, R, Nureki, O. | Deposit date: | 2013-09-05 | Release date: | 2013-10-30 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.953 Å) | Cite: | Structural and Functional Analyses of DNA-Sensing and Immune Activation by Human cGAS Plos One, 8, 2013
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4U4V
| Structure of a nitrate/nitrite antiporter NarK in apo inward-open state | Descriptor: | NICKEL (II) ION, Nitrate/nitrite transporter NarK, OLEIC ACID | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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4U4W
| Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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4U9L
| Structure of a membrane protein | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MAGNESIUM ION, Magnesium transporter MgtE | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-08-06 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE Nat Commun, 5, 2014
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4U9N
| Structure of a membrane protein | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MANGANESE (II) ION, Magnesium transporter MgtE, ... | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-08-06 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE Nat Commun, 5, 2014
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4U4T
| Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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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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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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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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4OO8
| Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3'), RNA (97-MER) | Authors: | Nishimasu, H, Ishitani, R, Nureki, O. | Deposit date: | 2014-01-31 | Release date: | 2014-02-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal structure of Cas9 in complex with guide RNA and target DNA Cell(Cambridge,Mass.), 156, 2014
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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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4P79
| Crystal structure of mouse claudin-15 | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Claudin-15 | Authors: | Suzuki, H, Nishizawa, T, Tani, K, Yamazaki, Y, Tamura, A, Ishitani, R, Dohmae, N, Tsukita, S, Nureki, O, Fujiyoshi, Y. | Deposit date: | 2014-03-26 | Release date: | 2014-04-30 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of a claudin provides insight into the architecture of tight junctions. Science, 344, 2014
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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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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: | 2011-12-14 | 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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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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3G5R
| Crystal structure of Thermus thermophilus TrmFO in complex with tetrahydrofolate | Descriptor: | (6S)-5,6,7,8-TETRAHYDROFOLATE, 1,2-ETHANEDIOL, CALCIUM ION, ... | 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 (1.6 Å) | Cite: | Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase Proc.Natl.Acad.Sci.USA, 106, 2009
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1UDZ
| Isoleucyl-tRNA synthetase editing domain | Descriptor: | Isoleucyl-tRNA synthetase | Authors: | Fukunaga, R, Fukai, S, Ishitani, R, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-05-08 | Release date: | 2004-03-23 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. J.Biol.Chem., 279, 2004
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1UE0
| Isoleucyl-tRNA synthetase editing domain complexed with L-Valine | Descriptor: | Isoleucyl-tRNA synthetase, VALINE | Authors: | Fukunaga, R, Fukai, S, Ishitani, R, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-05-08 | Release date: | 2004-03-23 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. J.Biol.Chem., 279, 2004
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