7VPJ
 
 | | Cryo-EM structure of the human ATP13A2 (E1P-ADP state) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Tomita, A, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-17 | | Release date: | 2021-12-29 | | Last modified: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2.
Mol.Cell, 81, 2021
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5GQJ
 | | Crystal structure of Cypovirus Polyhedra mutant with deletion of Ser193 and Ala194 | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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5GQM
 | | Crystal structure of in cellulo Wild Type Cypovirus Polyhedra | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, CYTIDINE-5'-TRIPHOSPHATE, ... | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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5GX4
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 14 MGy (12th measurement) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | Authors: | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | Deposit date: | 2016-09-15 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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2MLO
 | | Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membrane bound form | | Descriptor: | MCP-1 receptor | | Authors: | Esaki, K, Yoshinaga, S, Tsuji, T, Toda, E, Terashima, Y, Saitoh, T, Kohda, D, Kohno, T, Osawa, M, Ueda, T, Shimada, I, Matsushima, K, Terasawa, H. | | Deposit date: | 2014-03-04 | | Release date: | 2014-10-08 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Febs J., 281, 2014
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8HLB
 | | Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 | | Descriptor: | TR109 heavy chain, TR109 light chain, TR92 heavy chain, ... | | Authors: | Akiba, H, Fujita, J, Ise, T, Nishiyama, K, Miyata, T, Kato, T, Namba, K, Ohno, H, Kamada, H, Nagata, S, Tsumoto, K. | | Deposit date: | 2022-11-29 | | Release date: | 2023-10-04 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (3.63 Å) | | Cite: | Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection.
Commun Biol, 6, 2023
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2RVK
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2RVP
 | | Solution structure of DNA Containing Metallo-Base-Pair | | Descriptor: | DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION | | Authors: | Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y. | | Deposit date: | 2016-03-22 | | Release date: | 2016-08-31 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.
Chemistry, 22, 2016
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8OFY
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8OFX
 | | Molecular Mechanism of trypanosomal AQP2 | | Descriptor: | Aquaglyceroporin 2, [(2~{R},4~{S})-2-[4-[[4,6-bis(azanyl)-1,3,5-triazin-2-yl]amino]phenyl]-1,3,2-dithiarsolan-4-yl]methanol | | Authors: | Weyand, S.N, Matusevicius, M, Yamashita, K. | | Deposit date: | 2023-03-17 | | Release date: | 2024-10-02 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Molecular Mechanism of trypanosomal AQP2
To Be Published
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8OFZ
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7A4M
 | | Cryo-EM structure of mouse heavy-chain apoferritin at 1.22 A | | Descriptor: | FE (III) ION, Ferritin heavy chain, ZINC ION | | Authors: | Nakane, T, Kotecha, A, Sente, A, Yamashita, K, McMullan, G, Masiulis, S, Brown, P.M.G.E, Grigoras, I.T, Malinauskaite, L, Malinauskas, T, Miehling, J, Yu, L, Karia, D, Pechnikova, E.V, de Jong, E, Keizer, J, Bischoff, M, McCormack, J, Tiemeijer, P, Hardwick, S.W, Chirgadze, D.Y, Murshudov, G, Aricescu, A.R, Scheres, S.H.W. | | Deposit date: | 2020-08-20 | | Release date: | 2020-10-28 | | Last modified: | 2024-07-10 | | Method: | ELECTRON MICROSCOPY (1.22 Å) | | Cite: | Single-particle cryo-EM at atomic resolution.
Nature, 587, 2020
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1MKC
 | | C-TERMINAL DOMAIN OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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7A5V
 | | CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer, in complex with histamine and megabody Mb25 in lipid nanodisc | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | | Authors: | Nakane, T, Kotecha, A, Sente, A, Yamashita, K, McMullan, G, Masiulis, S, Brown, P.M.G.E, Grigoras, I.T, Malinauskaite, L, Malinauskas, T, Miehling, J, Yu, L, Karia, D, Pechnikova, E.V, de Jong, E, Keizer, J, Bischoff, M, McCormack, J, Tiemeijer, P, Hardwick, S.W, Chirgadze, D.Y, Murshudov, G, Aricescu, A.R, Scheres, S.H.W. | | Deposit date: | 2020-08-22 | | Release date: | 2020-11-18 | | Last modified: | 2020-11-25 | | Method: | ELECTRON MICROSCOPY (1.7 Å) | | Cite: | Single-particle cryo-EM at atomic resolution.
Nature, 587, 2020
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1EJ3
 | | CRYSTAL STRUCTURE OF AEQUORIN | | Descriptor: | AEQUORIN, C2-HYDROPEROXY-COELENTERAZINE | | Authors: | Head, J.F, Inouye, S, Teranishi, K, Shimomura, O. | | Deposit date: | 2000-02-29 | | Release date: | 2000-05-31 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The crystal structure of the photoprotein aequorin at 2.3 A resolution.
Nature, 405, 2000
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5GQK
 | | Crystal structure of Cypovirus Polyhedra mutant with deletion of Gly192-Ala194 | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Polyhedrin | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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5GQN
 | | Crystal structure of in cellulo Cypovirus Polyhedra mutant with deletion of Gly192-Ala194 | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Polyhedrin | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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2MLQ
 | | Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a frount bound form | | Descriptor: | MCP-1 receptor | | Authors: | Esaki, K, Yoshinaga, S, Tsuji, T, Toda, E, Terashima, Y, Saitoh, T, Kohda, D, Kohno, T, Osawa, M, Ueda, T, Shimada, I, Matsushima, K, Terasawa, H. | | Deposit date: | 2014-03-04 | | Release date: | 2014-10-08 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Febs J., 281, 2014
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1MKN
 | | N-TERMINAL HALF OF MIDKINE | | Descriptor: | PROTEIN (MIDKINE) | | Authors: | Iwasaki, W, Nagata, K, Hatanaka, H, Ogura, K, Inui, T, Kimura, T, Muramatsu, T, Yoshida, K, Tasumi, M, Inagaki, F. | | Deposit date: | 1999-03-16 | | Release date: | 1999-03-23 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of midkine, a new heparin-binding growth factor.
EMBO J., 16, 1997
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5THE
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5GUG
 | | Crystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain with inositol 1,4,5-trisphosphate | | Descriptor: | D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, Inositol 1,4,5-trisphosphate receptor type 1 | | Authors: | Hamada, K, Miyatake, H, Terauchi, A, Mikoshiba, K. | | Deposit date: | 2016-08-29 | | Release date: | 2017-04-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (7.399 Å) | | Cite: | IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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8H25
 | | Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230 | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Beta-galactosidase, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Saburi, W, Ota, T, Kato, K, Tagami, T, Yamashita, K, Yao, M, Mori, H. | | Deposit date: | 2022-10-04 | | Release date: | 2023-08-16 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2.295 Å) | | Cite: | Function and Structure of Lacticaseibacillus casei GH35 beta-Galactosidase LBCZ_0230 with High Hydrolytic Activity to Lacto- N -biose I and Galacto- N -biose.
J Appl Glycosci (1999), 70, 2023
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7VG7
 | | Plexin B1 extracellular fragment in complex with lasso-grafted PB1m6A9 peptide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Plexin-B1, TRIETHYLENE GLYCOL, ... | | Authors: | Sugano, N.N, Hirata, K, Yamashita, K, Yamamoto, M, Arimori, T, Takagi, J. | | Deposit date: | 2021-09-14 | | Release date: | 2022-08-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function.
Structure, 30, 2022
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7VF3
 | | Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, Plexin-B1, ... | | Authors: | Sugano, N.N, Hirata, K, Yamashita, K, Yamamoto, M, Arimori, T, Takagi, J. | | Deposit date: | 2021-09-10 | | Release date: | 2022-08-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function.
Structure, 30, 2022
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5VM9
 | | Human Argonaute3 bound to guide RNA | | Descriptor: | Protein argonaute-3, RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3'), RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*U)-3') | | Authors: | Park, M.S, Nakanishi, K. | | Deposit date: | 2017-04-26 | | Release date: | 2017-10-18 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.28 Å) | | Cite: | Human Argonaute3 has slicer activity.
Nucleic Acids Res., 45, 2017
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