PDB_ID PUBMED_CID STRUCTURE TITLE DEPOSITION DATE RELEASE DATE AUTHORS CITATION TITLE JOURNAL YEAR VOLUME FIRST PAGE LAST PAGE 3U2J 22248451 Neutron crystal structure of human Transthyretin 2011-10-03 2012-02-22 Yokoyama, T.,Mizuguchi, M.,Nabeshima, Y.,Kusaka, K.,Yamada, T.,Hosoya, T.,Ohhara, T.,Kurihara, K.,Tomoyori, K.,Tanaka, I.,Niimura, N. Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin J.Struct.Biol. 2012 177 283 290 4QCD 25872660 Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature. 2014-05-10 2015-04-29 Unno, M.,Ishikawa-Suto, K.,Kusaka, K.,Tamada, T.,Hagiwara, Y.,Sugishima, M.,Wada, K.,Yamada, T.,Tomoyori, K.,Hosoya, T.,Tanaka, I.,Niimura, N.,Kuroki, R.,Inaka, K.,Ishihara, M.,Fukuyama, K. Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography. J. Am. Chem. Soc. 2015 137 5452 5460 4QCD 25872660 Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature. 2014-05-10 2015-04-29 Unno, M.,Ishikawa-Suto, K.,Kusaka, K.,Tamada, T.,Hagiwara, Y.,Sugishima, M.,Wada, K.,Yamada, T.,Tomoyori, K.,Hosoya, T.,Tanaka, I.,Niimura, N.,Kuroki, R.,Inaka, K.,Ishihara, M.,Fukuyama, K. Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography. J. Am. Chem. Soc. 2015 137 5452 5460 5CG5 26314394 Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate 2015-07-09 2015-10-14 Yokoyama, T.,Mizuguchi, M.,Ostermann, A.,Kusaka, K.,Niimura, N.,Schrader, T.E.,Tanaka, I. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase J.Med.Chem. 2015 58 7549 7556 5CG5 26314394 Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate 2015-07-09 2015-10-14 Yokoyama, T.,Mizuguchi, M.,Ostermann, A.,Kusaka, K.,Niimura, N.,Schrader, T.E.,Tanaka, I. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase J.Med.Chem. 2015 58 7549 7556 6KK8 XN joint refinement of manganese catalase from Thermus Thermophilus HB27 2019-07-24 2019-09-04 Yamada, T.,Yano, N.,Hosoya, T.,Kusaka, K. Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27 J.Appl.Crystallogr. 2019 0 0 0 6KK8 XN joint refinement of manganese catalase from Thermus Thermophilus HB27 2019-07-24 2019-09-04 Yamada, T.,Yano, N.,Hosoya, T.,Kusaka, K. Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27 J.Appl.Crystallogr. 2019 0 0 0 6L46 32041886 High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans 2019-10-16 2020-02-12 Fukuda, Y.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc.Natl.Acad.Sci.USA 2020 117 4071 4077 6L46 32041886 High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans 2019-10-16 2020-02-12 Fukuda, Y.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc.Natl.Acad.Sci.USA 2020 117 4071 4077 6L9C 32371483 Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 2019-11-08 2020-04-29 Murakawa, T.,Kurihara, K.,Shoji, M.,Shibazaki, C.,Sunami, T.,Tamada, T.,Yano, N.,Yamada, T.,Kusaka, K.,Suzuki, M.,Shigeta, Y.,Kuroki, R.,Hayashi, H.,Yano, T.,Tanizawa, K.,Adachi, M.,Okajima, T. Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing. Proc.Natl.Acad.Sci.USA 2020 117 10818 10824 6L9C 32371483 Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 2019-11-08 2020-04-29 Murakawa, T.,Kurihara, K.,Shoji, M.,Shibazaki, C.,Sunami, T.,Tamada, T.,Yano, N.,Yamada, T.,Kusaka, K.,Suzuki, M.,Shigeta, Y.,Kuroki, R.,Hayashi, H.,Yano, T.,Tanizawa, K.,Adachi, M.,Okajima, T. Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing. Proc.Natl.Acad.Sci.USA 2020 117 10818 10824 7VEI 35647923 Neutron structure of D2O-solvent lysozyme 2021-09-08 2022-04-06 Chatake, T.,Tanaka, I.,Kusaka, K.,Fujiwara, S. Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography. Acta Crystallogr D Struct Biol 2022 78 770 778 7WNO 35546796 Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by only neutron diffraction data. 2022-01-19 2022-04-20 Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Iucrj 2022 9 342 348 7WNP 35546796 Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution. 2022-01-19 2022-04-20 Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Iucrj 2022 9 342 348 7WNP 35546796 Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution. 2022-01-19 2022-04-20 Murakawa, T.,Kurihara, K.,Adachi, M.,Kusaka, K.,Tanizawa, K.,Okajima, T. Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Iucrj 2022 9 342 348 7VOS 35594350 High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state 2021-10-14 2022-06-01 Hanazono, Y.,Hirano, Y.,Takeda, K.,Kusaka, K.,Tamada, T.,Miki, K. Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. Sci Adv 2022 8 0 0 7VOS 35594350 High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state 2021-10-14 2022-06-01 Hanazono, Y.,Hirano, Y.,Takeda, K.,Kusaka, K.,Tamada, T.,Miki, K. Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. Sci Adv 2022 8 0 0 7YKB 36463961 Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature 2022-07-22 2023-01-25 Joutsuka, T.,Nanasawa, R.,Igarashi, K.,Horie, K.,Sugishima, M.,Hagiwara, Y.,Wada, K.,Fukuyama, K.,Yano, N.,Mori, S.,Ostermann, A.,Kusaka, K.,Unno, M. Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states. J.Biol.Chem. 2022 299 102763 102763 7YKB 36463961 Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature 2022-07-22 2023-01-25 Joutsuka, T.,Nanasawa, R.,Igarashi, K.,Horie, K.,Sugishima, M.,Hagiwara, Y.,Wada, K.,Fukuyama, K.,Yano, N.,Mori, S.,Ostermann, A.,Kusaka, K.,Unno, M. Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states. J.Biol.Chem. 2022 299 102763 102763 7XVX Neutron crystal structure of human macrophage migration inhibitory factor 2022-05-25 2023-05-31 Ezawa, T.,Nakagaki, T.,Sugishima, K.,Ishida, T.,Hirano, Y.,Kusaka, K.,Tamada, T.,Odaka, M.,Wakui, H.,Matsumura, H. Neutron crystal structure of human macrophage migration inhibitory factor To Be Published 0 0 0 0 7XVX Neutron crystal structure of human macrophage migration inhibitory factor 2022-05-25 2023-05-31 Ezawa, T.,Nakagaki, T.,Sugishima, K.,Ishida, T.,Hirano, Y.,Kusaka, K.,Tamada, T.,Odaka, M.,Wakui, H.,Matsumura, H. Neutron crystal structure of human macrophage migration inhibitory factor To Be Published 0 0 0 0 7YQS 38382672 Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex 2022-08-08 2023-08-09 Yano, N.,Kondo, T.,Kusaka, K.,Arakawa, T.,Sakamoto, T.,Fushinobu, S. Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. J.Biol.Chem. 2024 300 105774 105774 7YQS 38382672 Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex 2022-08-08 2023-08-09 Yano, N.,Kondo, T.,Kusaka, K.,Arakawa, T.,Sakamoto, T.,Fushinobu, S. Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. J.Biol.Chem. 2024 300 105774 105774 8W6X 37712026 Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state 2023-08-30 2023-09-13 Hiromoto, T.,Nishikawa, K.,Inoue, S.,Ogata, H.,Hori, Y.,Kusaka, K.,Hirano, Y.,Kurihara, K.,Shigeta, Y.,Tamada, T.,Higuchi, Y. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase. Chem Sci 2023 14 9306 9315 8W6X 37712026 Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state 2023-08-30 2023-09-13 Hiromoto, T.,Nishikawa, K.,Inoue, S.,Ogata, H.,Hori, Y.,Kusaka, K.,Hirano, Y.,Kurihara, K.,Shigeta, Y.,Tamada, T.,Higuchi, Y. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase. Chem Sci 2023 14 9306 9315 8J6G Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0 2023-04-25 2023-09-20 Murakawa, T.,Kurihara, K.,Shoji, M.,Yano, N.,Kusaka, K.,Kawano, Y.,Suzuki, M.,Shigeta, Y.,Yano, T.,Adachi, M.,Tanizawa, K.,Okajima, T. Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor Acs Catalysis 2023 0 12403 12413 8J6G Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0 2023-04-25 2023-09-20 Murakawa, T.,Kurihara, K.,Shoji, M.,Yano, N.,Kusaka, K.,Kawano, Y.,Suzuki, M.,Shigeta, Y.,Yano, T.,Adachi, M.,Tanizawa, K.,Okajima, T. Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor Acs Catalysis 2023 0 12403 12413 8W48 37910439 Neutron and X-ray joint structure of WT-TTR in complex with piceatannol 2023-08-23 2023-11-22 Yokoyama, T.,Kusaka, K.,Mizuguchi, M.,Nabeshima, Y.,Fujiwara, S. Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin. J.Med.Chem. 2023 66 15511 15523 8W48 37910439 Neutron and X-ray joint structure of WT-TTR in complex with piceatannol 2023-08-23 2023-11-22 Yokoyama, T.,Kusaka, K.,Mizuguchi, M.,Nabeshima, Y.,Fujiwara, S. Resveratrol Derivatives Inhibit Transthyretin Fibrillization: Structural Insights into the Interactions between Resveratrol Derivatives and Transthyretin. J.Med.Chem. 2023 66 15511 15523 7YL8 Neutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature 2022-07-25 2024-02-07 Wada, K.,Kobayashi, K.,Era, I.,Isobe, Y.,Kamimura, T.,Marukawa, M.,Nagae, T.,Honjo, K.,Kaseda, N.,Motoyama, Y.,Inoue, K.,Sugishima, M.,Kusaka, K.,Yano, N.,Fukuyama, K.,Mishima, M.,Kitagawa, Y.,Unno, M. Protonation/deprotonation-driven switch for the redox stability of the low-potential [4Fe-4S] ferredoxin Elife 2025 0 0 0 7YL8 Neutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature 2022-07-25 2024-02-07 Wada, K.,Kobayashi, K.,Era, I.,Isobe, Y.,Kamimura, T.,Marukawa, M.,Nagae, T.,Honjo, K.,Kaseda, N.,Motoyama, Y.,Inoue, K.,Sugishima, M.,Kusaka, K.,Yano, N.,Fukuyama, K.,Mishima, M.,Kitagawa, Y.,Unno, M. Protonation/deprotonation-driven switch for the redox stability of the low-potential [4Fe-4S] ferredoxin Elife 2025 0 0 0 9KK7 39913263 Neutron structure of Ferredoxin-NADP+ reductase from maize root -Reduced form 2024-11-13 2025-01-29 Uenaka, M.,Ohnishi, Y.,Ise, A.,Yu, J.,Yano, N.,Kusaka, K.,Tanaka, H.,Kurisu, G. Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP + reductase revealed by high-resolution X-ray and neutron crystallography. Acta Crystallogr.,Sect.F 2025 81 73 84 9KKC 39913263 Neutron structure of Ferredoxin-NADP+ reductase from maize root -Oxidized form 2024-11-13 2025-01-29 Uenaka, M.,Ohnishi, Y.,Ise, A.,Yu, J.,Yano, N.,Kusaka, K.,Tanaka, H.,Kurisu, G. Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP + reductase revealed by high-resolution X-ray and neutron crystallography. Acta Crystallogr.,Sect.F 2025 81 73 84 8W4W Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4W Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4X Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4X Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4Y Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, low-D2O-solvent 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4Y Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, low-D2O-solvent 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4Z Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex, H2O solvent 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 8W4Z Neutron structure of cellulase Cel6A from Phanerochaete chrysosporium at room temperature, Enzyme-Product complex, H2O solvent 2023-08-25 2025-03-12 Tachioka, M.,Yamaguchi, S.,Nakamura, A.,Ishida, T.,Kusaka, K.,Yamada, T.,Yano, N.,Chatake, T.,Tamada, T.,Takeda, K.,Niwa, S.,Tanaka, H.,Takahashi, S.,Inaka, K.,Furubayashi, N.,Deguchi, S.,Samejima, M.,Igarashi, K. Deprotonated Arginine Controls a Putative Catalytic Base in Invert-ing Family 6 Glycoside Hydrolase To Be Published 0 0 0 0 9KVL 40436316 Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with nitrite 2024-12-05 2025-06-11 Fukuda, Y.,Lintuluoto, M.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. 2025 301 110290 110290 9KVL 40436316 Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with nitrite 2024-12-05 2025-06-11 Fukuda, Y.,Lintuluoto, M.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. 2025 301 110290 110290 9KVM 40436316 Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with formate 2024-12-05 2025-06-11 Fukuda, Y.,Lintuluoto, M.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. 2025 301 110290 110290 9KVM 40436316 Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with formate 2024-12-05 2025-06-11 Fukuda, Y.,Lintuluoto, M.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. 2025 301 110290 110290