2PJZ
| The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066 | Descriptor: | Hypothetical protein ST1066, SULFATE ION | Authors: | Hirata, K, Hasegawa, K, Ebihara, A, Yamamoto, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-04-17 | Release date: | 2008-04-22 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066 To be Published
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1WUA
| The structure of Aplyronine A-actin complex | Descriptor: | (8R,9R,10R,11R,14S,18S,20S,24S)-24-{(1R,2S,3R,6R,7R,8R,9S,10E)-8-(ACETYLOXY)-6-[(N,N-DIMETHYLALANYL)OXY]-11-[FORMYL(MET HYL)AMINO]-2-HYDROXY-1,3,7,9-TETRAMETHYLUNDEC-10-ENYL}-10-HYDROXY-14,20-DIMETHOXY-9,11,15,18-TETRAMETHYL-2-OXOOXACYCLOTE TRACOSA-3,5,15,21-TETRAEN-8-YL N,N,O-TRIMETHYLSERINATE, ADENOSINE-5'-TRIPHOSPHATE, Actin, ... | Authors: | Hirata, K, Muraoka, S, Suenaga, K, Kuroda, T, Kato, K, Tanaka, H, Yamamoto, M, Takata, M, Yamada, K, Kigoshi, H. | Deposit date: | 2004-12-03 | Release date: | 2006-02-14 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structure basis for antitumor effect of aplyronine a J.Mol.Biol., 356, 2006
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3WG7
| A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Hirata, K, Shinzawa-Itoh, K, Yano, N, Takemura, S, Kato, K, Hatanaka, M, Muramoto, K, Kawahara, T, Tsukihara, T, Yamashita, E, Tono, K, Ueno, G, Hikima, T, Murakami, H, Inubushi, Y, Yabashi, M, Ishikawa, T, Yamamoto, M, Ogura, T, Sugimoto, H, Shen, J.R, Yoshikawa, S, Ago, H. | Deposit date: | 2013-07-29 | Release date: | 2014-04-30 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nat.Methods, 11, 2014
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7Y44
| Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | Authors: | Tsukihara, T, Hirata, K, Ago, H. | Deposit date: | 2022-06-14 | Release date: | 2022-07-20 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Nat.Methods, 11, 2014
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5AYG
| Crystal Structure of the Human ROR gamma Ligand Binding Domain With 3g | Descriptor: | 3-[5-(2-cyclohexylethyl)-4-ethyl-1,2,4-triazol-3-yl]-N-naphthalen-1-yl-propanamide, Nuclear receptor ROR-gamma | Authors: | Noguchi, M, Doi, S, Nomura, A, Kikuwaka, M, Murase, K, Hirata, K, Kamada, M, Adachi, T. | Deposit date: | 2015-08-20 | Release date: | 2016-03-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | SAR Exploration Guided by LE and Fsp(3): Discovery of a Selective and Orally Efficacious ROR gamma Inhibitor Acs Med.Chem.Lett., 7, 2016
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4UB8
| Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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4UB6
| Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | Deposit date: | 2014-08-12 | Release date: | 2014-12-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses. Nature, 517, 2015
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8X8V
| Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment | Descriptor: | Polyhedrin,Myc proto-oncogene protein | Authors: | Kojima, M, Ueno, T, Abe, S, Hirata, K. | Deposit date: | 2023-11-29 | Release date: | 2024-06-05 | Last modified: | 2024-07-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc.Natl.Acad.Sci.USA, 121, 2024
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8X8S
| Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment | Descriptor: | Polyhedrin,Myc proto-oncogene protein | Authors: | Kojima, M, Ueno, T, Abe, S, Hirata, K. | Deposit date: | 2023-11-28 | Release date: | 2024-06-05 | Last modified: | 2024-07-03 | Method: | X-RAY DIFFRACTION (2.04 Å) | Cite: | High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc.Natl.Acad.Sci.USA, 121, 2024
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8GQ1
| HyHEL10 Fab complexed with hen egg lysozyme carrying arginine cluster in framework region of light chain. | Descriptor: | Heavy Chain of HyHel10 Antibody Fragment (Fab), Light Chain of HyHel10 Antibody Fragment (Fab), Lysozyme C, ... | Authors: | Matsuura, H, Hirata, K, Sakai, N, Nakakido, M, Tsumoto, K. | Deposit date: | 2022-08-28 | Release date: | 2023-08-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.13 Å) | Cite: | Arginine cluster introduction on framework region in anti-lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops. Protein Sci., 32, 2023
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8W7N
| Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis | Descriptor: | Pesticidal crystal protein Cry1Aa, UNKNOWN ATOM OR ION | Authors: | Tanaka, J, Abe, S, Hayakawa, T, Kojima, M, Yamashita, K, Hirata, K, Ueno, T. | Deposit date: | 2023-08-31 | Release date: | 2024-03-06 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis. Biochem.Biophys.Res.Commun., 685, 2023
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5ONY
| As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2017-08-04 | Release date: | 2017-11-29 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase. IUCrJ, 5, 2018
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5ONX
| Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2017-08-04 | Release date: | 2017-11-29 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase. IUCrJ, 5, 2018
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6E67
| Structure of beta2 adrenergic receptor fused to a Gs peptide | Descriptor: | 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one, Beta-2 adrenergic receptor,Endolysin,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Beta-2 adrenergic receptor chimera | Authors: | Liu, X, Xu, X, Hilger, D, Tiemann, J, Liu, H, Du, Y, Hirata, K, Sun, X, Guixa-Gonzalez, R, Mathiesen, J, Hildebrand, P, Kobilka, B. | Deposit date: | 2018-07-24 | Release date: | 2019-06-05 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.7 Å) | Cite: | Structural Insights into the Process of GPCR-G Protein Complex Formation. Cell, 177, 2019
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8WLG
| Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment | Descriptor: | Polyhedrin,Myc proto-oncogene protein | Authors: | Kojima, M, Ueno, T, Abe, S, Hirata, K. | Deposit date: | 2023-09-29 | Release date: | 2024-06-05 | Last modified: | 2024-07-03 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc.Natl.Acad.Sci.USA, 121, 2024
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6N48
| Structure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator | Descriptor: | (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate, 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one, Camelid Antibody Fragment, ... | Authors: | Liu, X, Masoudi, A, Kahsai, A.W, Huang, L.Y, Pani, B, Hirata, K, Ahn, S, Lefkowitz, R.J, Kobilka, B.K. | Deposit date: | 2018-11-17 | Release date: | 2019-06-26 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.2 Å) | Cite: | Mechanism of beta2AR regulation by an intracellular positive allosteric modulator. Science, 364, 2019
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8J2Q
| Crystal structure of Cypovirus Polyhedra mutant fused with c-Myc fragment | Descriptor: | Polyhedrin,Myc proto-oncogene protein | Authors: | Kojima, M, Ueno, T, Abe, S, Hirata, K. | Deposit date: | 2023-04-15 | Release date: | 2024-04-17 | Last modified: | 2024-07-03 | Method: | X-RAY DIFFRACTION (1.92 Å) | Cite: | High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc.Natl.Acad.Sci.USA, 121, 2024
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8JAE
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6OBA
| The beta2 adrenergic receptor bound to a negative allosteric modulator | Descriptor: | (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol, 6-bromo-N~2~-phenylquinazoline-2,4-diamine, Beta-2 adrenergic receptor,Lysozyme,Beta-2 adrenergic receptor, ... | Authors: | Liu, X, Stobel, A, Kaindl, J, Dengler, D, ClarK, M, Mahoney, J, Korczynska, M, Matt, R.A, Hubner, H, Xu, X, Stanek, M, Hirata, K, Shoichet, B, Sunahara, R, Gmeiner, R, Kobilka, B.K. | Deposit date: | 2019-03-20 | Release date: | 2020-03-25 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | An allosteric modulator binds to a conformational hub in the beta2adrenergic receptor. Nat.Chem.Biol., 16, 2020
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6ZAV
| NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX) | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.19 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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6ZAW
| Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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6ZAR
| As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX) | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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6ZAX
| Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy) | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.48 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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6ZAU
| Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.3 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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6ZAT
| Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.0 A resolution (unrestrained full matrix refinement by SHELX) | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | Deposit date: | 2020-06-05 | Release date: | 2021-01-20 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Sci Adv, 7, 2021
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