8HRX
 
 | | Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex | | Descriptor: | Fab heavy chain from antibody IgG clone number YN9048, Fab light chain from antibody IgG clone number YN9048, PreS1 protein (Fragment), ... | | Authors: | Asami, J, Shimizu, T, Ohto, U. | | Deposit date: | 2022-12-16 | | Release date: | 2024-01-17 | | Last modified: | 2024-04-03 | | Method: | ELECTRON MICROSCOPY (2.89 Å) | | Cite: | Structural basis of hepatitis B virus receptor binding.
Nat.Struct.Mol.Biol., 31, 2024
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8HRY
 | | Cryo-EM structure of human NTCP-myr-preS1-YN9016Fab complex | | Descriptor: | Fab heavy chain from antibody IgG clone number YN9016, Fab light chain from antibody IgG clone number YN9016, Large S protein (Fragment), ... | | Authors: | Asami, J, Shimizu, T, Ohto, U. | | Deposit date: | 2022-12-16 | | Release date: | 2024-01-17 | | Last modified: | 2024-04-03 | | Method: | ELECTRON MICROSCOPY (3.11 Å) | | Cite: | Structural basis of hepatitis B virus receptor binding.
Nat.Struct.Mol.Biol., 31, 2024
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7C77
 | | Cryo-EM structure of mouse TLR3 in complex with UNC93B1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Protein unc-93 homolog B1, ... | | Authors: | Ohto, U, Ishida, H, Shimizu, T. | | Deposit date: | 2020-05-23 | | Release date: | 2021-01-06 | | Last modified: | 2021-02-24 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Cryo-EM structures of Toll-like receptors in complex with UNC93B1.
Nat.Struct.Mol.Biol., 28, 2021
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7C76
 | | Cryo-EM structure of human TLR3 in complex with UNC93B1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Protein unc-93 homolog B1, ... | | Authors: | Ohto, U, Ishida, H, Shimizu, T. | | Deposit date: | 2020-05-23 | | Release date: | 2021-01-06 | | Last modified: | 2021-02-24 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Cryo-EM structures of Toll-like receptors in complex with UNC93B1.
Nat.Struct.Mol.Biol., 28, 2021
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7CRF
 | | Crystal structure of human TLR8 in complex with CU-CPD107 | | Descriptor: | 1-[2-(ethoxymethyl)-4-iodanyl-5-phenyl-imidazol-1-yl]-2-methyl-propan-2-ol, 2-acetamido-2-deoxy-beta-D-glucopyranose, Toll-like receptor 8, ... | | Authors: | Sakaniwa, K, Tanji, H, Ohto, U, Shimizu, T. | | Deposit date: | 2020-08-13 | | Release date: | 2021-06-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.89 Å) | | Cite: | Tetrasubstituted imidazoles as incognito Toll-like receptor 8 a(nta)gonists.
Nat Commun, 12, 2021
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7CYN
 | | Cryo-EM structure of human TLR7 in complex with UNC93B1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Protein unc-93 homolog B1, ... | | Authors: | Ohto, U, Ishida, H, Shimizu, T. | | Deposit date: | 2020-09-03 | | Release date: | 2021-01-06 | | Last modified: | 2021-02-24 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Cryo-EM structures of Toll-like receptors in complex with UNC93B1.
Nat.Struct.Mol.Biol., 28, 2021
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5WRD
 | | Crystal structure of LC3B in complex with FYCO1 LIR | | Descriptor: | GLYCEROL, Microtubule-associated proteins 1A/1B light chain 3B, Peptide from FYVE and coiled-coil domain-containing protein 1 | | Authors: | Sakurai, S, Ohto, U, Shimizu, T. | | Deposit date: | 2016-12-01 | | Release date: | 2017-03-29 | | Last modified: | 2020-02-26 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif
Acta Crystallogr F Struct Biol Commun, 73, 2017
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5GID
 | | Crystal structure of VDR in complex with DLAM-4 (C2 form) | | Descriptor: | (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one, SRC1, Vitamin D3 receptor | | Authors: | Asano, L, Shimizu, T. | | Deposit date: | 2016-06-23 | | Release date: | 2016-12-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.151 Å) | | Cite: | Regulation of the vitamin D receptor by vitamin D lactam derivatives.
Febs Lett., 590, 2016
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5GIE
 | | Crystal structure of VDR in complex with DLAM-4P (P21 form) | | Descriptor: | (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one, SRC1, Vitamin D3 receptor | | Authors: | Asano, L, Shimizu, T. | | Deposit date: | 2016-06-23 | | Release date: | 2016-12-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.387 Å) | | Cite: | Regulation of the vitamin D receptor by vitamin D lactam derivatives.
Febs Lett., 590, 2016
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8ISN
 | | HLA-A24 in complex with modified 9mer WT1 peptide | | Descriptor: | Beta-2-microglobulin, CYS-TYR-THR-TRP-ASN-GLN-MET-ASN-LEU, GLYCEROL, ... | | Authors: | Bekker, G.J, Numoto, N, Kawasaki, M, Hayashi, T, Yabuno, S, Kozono, Y, Shimizu, T, Kozono, H, Ito, N, Oda, M, Kamiya, N. | | Deposit date: | 2023-03-21 | | Release date: | 2023-09-13 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.48 Å) | | Cite: | Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.
Protein Sci., 32, 2023
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5HDH
 | | Crystal structure of human TLR8 with an uncleaved Z-loop | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Tanji, H, Ohto, U, Shimizu, T. | | Deposit date: | 2016-01-05 | | Release date: | 2016-03-09 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Autoinhibition and relief mechanism by the proteolytic processing of Toll-like receptor 8
Proc.Natl.Acad.Sci.USA, 113, 2016
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5IRN
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5IRM
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5IRL
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5XGC
 | | Crystal structure of SmgGDS-558 | | Descriptor: | Rap1 GTPase-GDP dissociation stimulator 1 | | Authors: | Shimizu, H, Toma-Fukai, S, Shimizu, T. | | Deposit date: | 2017-04-13 | | Release date: | 2017-06-28 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding
J. Biol. Chem., 292, 2017
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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
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3A57
 | | Crystal structure of Thermostable Direct Hemolysin | | Descriptor: | Thermostable direct hemolysin 2 | | Authors: | Hashimoto, H, Yanagihara, I, Nakahira, K, Hamada, D, Ikegami, T, Mayanagi, K, Kaieda, S, Fukui, T, Ohnishi, K, Kajiyama, S, Yamane, T, Ikeguchi, M, Honda, T, Shimizu, T, Sato, M. | | Deposit date: | 2009-08-03 | | Release date: | 2010-03-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin
J.Biol.Chem., 285, 2010
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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
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5ZHX
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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
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5WYZ
 | | Crystal structure of human TLR8 in complex with CU-CPT9b | | 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-(3-methyl-4-oxidanyl-phenyl)quinolin-7-ol, ... | | 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 (2.3 Å) | | Cite: | Small-molecule inhibition of TLR8 through stabilization of its resting state
Nat. Chem. Biol., 14, 2018
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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
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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
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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
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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
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