7WM4
| Cryo-EM structure of tetrameric TLR3 in complex with dsRNA (90 bp) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RNA (81-MER), ... | Authors: | Sakaniwa, K, Ohto, U, Shimizu, T. | Deposit date: | 2022-01-14 | Release date: | 2023-01-25 | Last modified: | 2023-08-30 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction. Nat Commun, 14, 2023
|
|
7VTQ
| Cryo-EM structure of mouse NLRP3 (full-length) dodecamer | Descriptor: | 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea, ADENOSINE-5'-DIPHOSPHATE, NACHT, ... | Authors: | Ohto, U, Shimizu, T. | Deposit date: | 2021-10-30 | Release date: | 2022-03-09 | Last modified: | 2022-03-23 | Method: | ELECTRON MICROSCOPY (3.55 Å) | Cite: | Structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation. Proc.Natl.Acad.Sci.USA, 119, 2022
|
|
5XDR
| Crystal structure of human DEAH-box RNA helicase DHX15 in complex with ADP | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15, ... | Authors: | Murakami, K, Nakano, K, Shimizu, T, Ohto, U. | Deposit date: | 2017-03-29 | Release date: | 2017-06-21 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The crystal structure of human DEAH-box RNA helicase 15 reveals a domain organization of the mammalian DEAH/RHA family Acta Crystallogr F Struct Biol Commun, 73, 2017
|
|
5YAQ
| Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with scyllo-inosose | Descriptor: | (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Authors: | Fukano, K, Shimizu, T, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2017-09-01 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification PLoS ONE, 13, 2018
|
|
5YAB
| Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Descriptor: | ACETATE ION, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Authors: | Fukano, K, Shimizu, T, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2017-08-31 | Release date: | 2018-05-23 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification PLoS ONE, 13, 2018
|
|
5YAP
| Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with L-glucono-1,5-lactone | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, L-glucono-1,5-lactone, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Authors: | Fukano, K, Shimizu, T, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2017-09-01 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification PLoS ONE, 13, 2018
|
|
5Y7Y
| Crystal structure of AhRR/ARNT complex | Descriptor: | Aryl hydrocarbon receptor nuclear translocator, Aryl hydrocarbon receptor repressor, GLYCEROL | Authors: | Sakurai, S, Shimizu, T, Ohto, U. | Deposit date: | 2017-08-18 | Release date: | 2017-09-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | The crystal structure of the AhRR-ARNT heterodimer reveals the structural basis of the repression of AhR-mediated transcription. J. Biol. Chem., 292, 2017
|
|
5YA8
| Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol | Descriptor: | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity | Authors: | Fukano, K, Shimizu, T, Sasaki, Y, Nakamura, A, Yajima, S. | Deposit date: | 2017-08-31 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification PLoS ONE, 13, 2018
|
|
5Z15
| Crystal structure of human TLR8 in complex with CU-CPT9c | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(7-chloranylquinolin-4-yl)-2-methyl-phenol, ... | Authors: | Tanji, H, Ohto, U, Shimizu, T. | Deposit date: | 2017-12-25 | Release date: | 2018-07-04 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Inhibition of Toll-like Receptor 8 by Specifically Targeting a Unique Allosteric Site and Locking Its Resting State To Be Published
|
|
5Z14
| Crystal structure of human TLR8 in complex with CU-CPT9a | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(7-methoxyquinolin-4-yl)-2-methyl-phenol, ... | Authors: | Tanji, H, Ohto, U, Shimizu, T. | Deposit date: | 2017-12-25 | Release date: | 2018-07-04 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Inhibition of Toll-like Receptor 8 by Specifically Targeting a Unique Allosteric Site and Locking Its Resting State To Be Published
|
|
5WYX
| Crystal structure of human TLR8 in complex with CU-CPT8m | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 7-(3-methylphenyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide, ... | Authors: | Tanji, H, Ohto, U, Shimizu, T. | Deposit date: | 2017-01-16 | Release date: | 2017-12-13 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Small-molecule inhibition of TLR8 through stabilization of its resting state Nat. Chem. Biol., 14, 2018
|
|
7WGE
| Human NLRP1 complexed with thioredoxin | Descriptor: | MAGNESIUM ION, NACHT, LRR and PYD domains-containing protein 1, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2021-12-28 | Release date: | 2023-07-05 | Last modified: | 2023-10-18 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structural basis for thioredoxin-mediated suppression of NLRP1 inflammasome. Nature, 622, 2023
|
|
7VTP
| Cryo-EM structure of PYD-deleted human NLRP3 hexamer | Descriptor: | 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea, ADENOSINE-5'-DIPHOSPHATE, NACHT, ... | Authors: | Ohto, U, Shimizu, T. | Deposit date: | 2021-10-30 | Release date: | 2022-03-09 | Last modified: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (3.23 Å) | Cite: | Structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation. Proc.Natl.Acad.Sci.USA, 119, 2022
|
|
7WBU
| Cryo-EM structure of bovine NLRP9 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, NACHT, LRR and PYD domains-containing protein 9 | Authors: | Kamitsukasa, Y, Shimizu, T, Ohto, U. | Deposit date: | 2021-12-17 | Release date: | 2022-04-06 | Last modified: | 2024-06-26 | Method: | ELECTRON MICROSCOPY (3.42 Å) | Cite: | The structure of NLRP9 reveals a unique C-terminal region with putative regulatory function. Febs Lett., 596, 2022
|
|
7WBT
| Crystal structure of bovine NLRP9 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, NACHT, LRR and PYD domains-containing protein 9 | Authors: | Kamitsukasa, Y, Shimizu, T, Ohto, U. | Deposit date: | 2021-12-17 | Release date: | 2022-04-06 | Last modified: | 2022-04-27 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | The structure of NLRP9 reveals a unique C-terminal region with putative regulatory function. Febs Lett., 596, 2022
|
|
5IRM
| |
5IRL
| |
6LVY
| Crystal structure of TLR7/Cpd-2 (SM-360320) complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-(2-methoxyethoxy)-9-(phenylmethyl)-7H-purin-8-one, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2020-02-06 | Release date: | 2020-11-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun, 11, 2020
|
|
6LW0
| Crystal structure of TLR7/Cpd-6 (DSR-139293) complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purin-6-amine, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2020-02-06 | Release date: | 2020-11-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun, 11, 2020
|
|
6LVZ
| Crystal structure of TLR7/Cpd-3 (SM-394830) complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-(2-methoxyethoxy)-9-(pyridin-3-ylmethyl)-7H-purin-8-one, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2020-02-06 | Release date: | 2020-11-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.83 Å) | Cite: | Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun, 11, 2020
|
|
6LVX
| Crystal structure of TLR7/Cpd-1 (SM-374527) complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 6-azanyl-2-butoxy-9-(phenylmethyl)-7H-purin-8-one, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2020-02-06 | Release date: | 2020-11-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.77 Å) | Cite: | Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun, 11, 2020
|
|
6IR4
| Crystal structure of BioU from Synechocystis sp.PCC6803 (apo form) | Descriptor: | Slr0355 protein | Authors: | Sakaki, K, Oishi, K, Shimizu, T, Tomita, T, Kuzuyama, T, Nishiyama, M. | Deposit date: | 2018-11-10 | Release date: | 2020-01-15 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat.Chem.Biol., 16, 2020
|
|
6IF5
| Crystal structure of monkey TLR7 in complex with 2',3'-cGMP (Guanosine 2',3'-cyclic phosphate) | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GUANOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE, ... | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2018-09-18 | Release date: | 2019-01-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Cell Rep, 25, 2018
|
|
6LW1
| Cryo-EM structure of TLR7/Cpd-7 (DSR-139970) complex in open form | Descriptor: | 2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine, Toll-like receptor 7 | Authors: | Zhang, Z, Ohto, U, Shimizu, T. | Deposit date: | 2020-02-06 | Release date: | 2020-11-11 | Method: | ELECTRON MICROSCOPY (2.8 Å) | Cite: | Structural analysis reveals TLR7 dynamics underlying antagonism. Nat Commun, 11, 2020
|
|
6IU1
| |