1UIG
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8JF5
| Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440 | Descriptor: | 4-[5-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-2-[2-fluoranyl-4-(2-methyl-2-oxidanyl-propyl)phenyl]phenyl]-2-fluoranyl-benzenecarbonitrile, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Fukushima, H, Machida, T, Yamashita, S, Suzuki, T. | Deposit date: | 2023-05-17 | Release date: | 2024-05-22 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | TAS1440, a histone H3 competitive LSD1 inhibitor, activates both TGF-beta and notch signaling pathways via INSM1 dissociation in neuroendocrine small cell lung cancer To Be Published
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2E2P
| Crystal structure of Sulfolobus tokodaii hexokinase in complex with ADP | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADENOSINE-5'-DIPHOSPHATE, HEXOKINASE, ... | Authors: | Nishimasu, H, Fushinobu, S, Shoun, H, Wakagi, T. | Deposit date: | 2006-11-15 | Release date: | 2007-01-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J.Biol.Chem., 282, 2007
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2E2Q
| Crystal structure of Sulfolobus tokodaii hexokinase in complex with xylose, Mg2+, and ADP | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, HEXOKINASE, MAGNESIUM ION, ... | Authors: | Nishimasu, H, Fushinobu, S, Shoun, H, Wakagi, T. | Deposit date: | 2006-11-15 | Release date: | 2007-01-16 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J.Biol.Chem., 282, 2007
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2E2N
| Crystal structure of Sulfolobus tokodaii hexokinase in the apo form | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, HEXOKINASE, SULFATE ION | Authors: | Nishimasu, H, Fushinobu, S, Shoun, H, Wakagi, T. | Deposit date: | 2006-11-15 | Release date: | 2007-01-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J.Biol.Chem., 282, 2007
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2E2O
| Crystal structure of Sulfolobus tokodaii hexokinase in complex with glucose | Descriptor: | HEXOKINASE, beta-D-glucopyranose | Authors: | Nishimasu, H, Fushinobu, S, Shoun, H, Wakagi, T. | Deposit date: | 2006-11-15 | Release date: | 2007-01-16 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structures of an ATP-dependent hexokinase with broad substrate specificity from the hyperthermophilic archaeon Sulfolobus tokodaii. J.Biol.Chem., 282, 2007
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1J2E
| Crystal structure of Human Dipeptidyl peptidase IV | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase IV | Authors: | Hiramatsu, H, Kyono, K, Higashiyama, Y, Fukushima, C, Shima, H, Sugiyama, S, Inaka, K, Yamamoto, A, Shimizu, R. | Deposit date: | 2002-12-30 | Release date: | 2003-12-30 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller fold. Biochem.Biophys.Res.Commun., 302, 2003
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1WCY
| Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Diprotin A | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Dipeptidyl peptidase IV, ... | Authors: | Hiramatsu, H, Yamamoto, A, Kyono, K, Higashiyama, Y, Fukushima, C, Shima, H, Sugiyama, S, Inaka, K, Shimizu, R. | Deposit date: | 2004-05-07 | Release date: | 2005-05-07 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | The crystal structure of human dipeptidyl peptidase IV (DPPIV) complex with diprotin A Biol.Chem., 385, 2004
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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: | 2023-11-29 | 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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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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8ZH8
| Human GPR103 -Gq complex bound to QRFP26 | Descriptor: | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | Authors: | Iwama, A, Akasaka, H, Sano, F.K, Oshima, H.S, Shihoya, W, Nureki, O. | Deposit date: | 2024-05-10 | Release date: | 2024-07-03 | Method: | ELECTRON MICROSCOPY (3.19 Å) | Cite: | Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103. Nat Commun, 15, 2024
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8WT9
| Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction resolution) | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | Deposit date: | 2023-10-18 | Release date: | 2024-06-26 | Last modified: | 2024-07-17 | Method: | ELECTRON MICROSCOPY (2.7 Å) | Cite: | Structural mechanism of bridge RNA-guided recombination. Nature, 630, 2024
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8WT7
| Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange locked state | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | Deposit date: | 2023-10-18 | Release date: | 2024-06-26 | Last modified: | 2024-07-17 | Method: | ELECTRON MICROSCOPY (2.7 Å) | Cite: | Structural mechanism of bridge RNA-guided recombination. Nature, 630, 2024
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8WT8
| Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate) | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | Deposit date: | 2023-10-18 | Release date: | 2024-06-26 | Last modified: | 2024-07-17 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Structural mechanism of bridge RNA-guided recombination. Nature, 630, 2024
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8WT6
| Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange state | Descriptor: | IS621 transposase, MAGNESIUM ION, bridge RNA, ... | Authors: | Hiraizumi, M, Yamashita, K, Nishimasu, H. | Deposit date: | 2023-10-18 | Release date: | 2024-06-26 | Last modified: | 2024-07-17 | Method: | ELECTRON MICROSCOPY (2.5 Å) | Cite: | Structural mechanism of bridge RNA-guided recombination. Nature, 630, 2024
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7E6Z
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 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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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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7E6X
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms 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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7E70
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 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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7E71
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms 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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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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8X5V
| BlCas9-sgRNA-target DNA complex | Descriptor: | 1,2-ETHANEDIOL, BlCas9, CHLORIDE ION, ... | Authors: | Nakane, T, Nakagawa, R, Yamashita, K, Nishimasu, H, Nureki, O. | Deposit date: | 2023-11-19 | Release date: | 2024-07-10 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure and engineering of Brevibacillus laterosporus Cas9. Commun Biol, 7, 2024
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5HRT
| Crystal structure of mouse autotaxin in complex with a DNA aptamer | Descriptor: | CALCIUM ION, CHLORIDE ION, Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, ... | Authors: | Kato, K, Nishimasu, H, Morita, J, Ishitani, R, Nureki, O. | Deposit date: | 2016-01-24 | Release date: | 2016-04-06 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Structural basis for specific inhibition of Autotaxin by a DNA aptamer Nat.Struct.Mol.Biol., 23, 2016
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2DCT
| Crystal structure of the TT1209 from Thermus thermophilus HB8 | Descriptor: | CHLORIDE ION, SODIUM ION, hypothetical protein TTHA0104 | Authors: | Asada, Y, Sugahara, M, Shimizu, K, Yamamoto, H, Shimada, H, Nakamoto, T, Ono, N, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-01-12 | Release date: | 2006-01-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Crystal structure of the TT1209 from Thermus thermophilus HB8 To be Published
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8GS2
| Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex | Descriptor: | ADENOSINE MONOPHOSPHATE, CHAT domain-containing protein, CRISPR-associated RAMP family protein, ... | Authors: | Kato, K, Okazaki, S, Ishikawa, J, Isayama, Y, Nishizawa, T, Nishimasu, H. | Deposit date: | 2022-09-04 | Release date: | 2022-11-09 | Last modified: | 2024-05-29 | Method: | ELECTRON MICROSCOPY (2.84 Å) | Cite: | RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Science, 378, 2022
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