4U4V
| Structure of a nitrate/nitrite antiporter NarK in apo inward-open state | Descriptor: | NICKEL (II) ION, Nitrate/nitrite transporter NarK, OLEIC ACID | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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4U4W
| Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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4U4T
| Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | Deposit date: | 2014-07-24 | Release date: | 2015-07-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK Nat Commun, 6, 2015
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4XQ1
| Crystal structure of hemerythrin: L114A mutant | Descriptor: | Bacteriohemerythrin, FE (III) ION, NITRATE ION, ... | Authors: | Chuankhayan, P, Chen, K.H.C, Wu, H.H, Chen, C.J, Fukuda, M, Yu, S.S.F, Chan, S.I. | Deposit date: | 2015-01-18 | Release date: | 2015-04-29 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel. J.Inorg.Biochem., 150, 2015
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4XPW
| Crystal structures of Leu114F mutant | Descriptor: | Bacteriohemerythrin, FE (II) ION, GLYCEROL | Authors: | Chuankhayan, P, Chen, K.H.C, Wu, H.H, Chen, C.J, Fukuda, M, Yu, S.S.F, Chan, S.I. | Deposit date: | 2015-01-18 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.17 Å) | Cite: | The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel. J.Inorg.Biochem., 150, 2015
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4XPY
| Crystal structure of hemerythrin : L114Y mutant | Descriptor: | Bacteriohemerythrin, FE (II) ION, GLYCEROL | Authors: | Chuankhayan, P, Chen, K.H.C, Wu, H.H, Chen, C.J, Fukuda, M, Yu, S.S.F, Chan, S.I. | Deposit date: | 2015-01-18 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.13 Å) | Cite: | The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel. J.Inorg.Biochem., 150, 2015
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4XPX
| Crystal structure of hemerythrin:wild-type | Descriptor: | Bacteriohemerythrin, FE (II) ION | Authors: | Chuankhayan, P, Chen, K.H.C, Wu, H.H, Chen, C.J, Fukuda, M, Yu, S.S.F, Chan, S.I. | Deposit date: | 2015-01-18 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.03 Å) | Cite: | The bacteriohemerythrin from Methylococcus capsulatus (Bath): Crystal structures reveal that Leu114 regulates a water tunnel. J.Inorg.Biochem., 150, 2015
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8H86
| Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR1 in lipid nanodisc | Descriptor: | (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, HcKCR1, PALMITIC ACID, ... | Authors: | Tajima, S, Kim, Y, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | Deposit date: | 2022-10-21 | Release date: | 2023-09-06 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.56 Å) | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell, 186, 2023
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8H87
| Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR2 in lipid nanodisc | Descriptor: | (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, HcKCR2, PALMITIC ACID, ... | Authors: | Tajima, S, Kim, Y, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | Deposit date: | 2022-10-21 | Release date: | 2023-09-06 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.53 Å) | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell, 186, 2023
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8IU0
| Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR1 H225F mutant in lipid nanodisc | Descriptor: | (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, HcKCR1, PALMITIC ACID, ... | Authors: | Tajima, S, Kim, Y, Nakamura, S, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | Deposit date: | 2023-03-23 | Release date: | 2023-09-06 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.66 Å) | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell, 186, 2023
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1F3P
| FERREDOXIN REDUCTASE (BPHA4)-NADH COMPLEX | Descriptor: | FERREDOXIN REDUCTASE, FLAVIN-ADENINE DINUCLEOTIDE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | Authors: | Senda, T, Yamada, T, Sakurai, N, Kubota, M, Nishizaki, T, Masai, E, Fukuda, M, Mitsuidagger, Y. | Deposit date: | 2000-06-06 | Release date: | 2001-06-06 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J.Mol.Biol., 304, 2000
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1ULI
| Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1 | Descriptor: | FE (II) ION, FE2/S2 (INORGANIC) CLUSTER, biphenyl dioxygenase large subunit, ... | Authors: | Furusawa, Y, Nagarajan, V, Masai, E, Tanokura, M, Fukuda, M, Senda, T. | Deposit date: | 2003-09-12 | Release date: | 2004-09-28 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1 J.Mol.Biol., 342, 2004
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1ULJ
| Biphenyl dioxygenase (BphA1A2) in complex with the substrate | Descriptor: | BIPHENYL, FE (II) ION, FE2/S2 (INORGANIC) CLUSTER, ... | Authors: | Furusawa, Y, Nagarajan, V, Masai, E, Tanokura, M, Fukuda, M, Senda, T. | Deposit date: | 2003-09-12 | Release date: | 2004-09-28 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1 J.Mol.Biol., 342, 2004
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1D7Y
| CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4 | Descriptor: | FERREDOXIN REDUCTASE, FLAVIN-ADENINE DINUCLEOTIDE | Authors: | Senda, T, Yamada, T, Sakurai, N, Kubota, M, Nishizaki, T, Masai, E, Fukuda, M, Mitsui, Y. | Deposit date: | 1999-10-21 | Release date: | 2000-12-20 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J.Mol.Biol., 304, 2000
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2ZET
| Crystal structure of the small GTPase Rab27B complexed with the Slp homology domain of Slac2-a/melanophilin | Descriptor: | GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Melanophilin, ... | Authors: | Kukimoto-Niino, M, Sakamoto, A, Kanno, E, Hanawa-Suetsugu, K, Terada, T, Shirouzu, M, Fukuda, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-12-17 | Release date: | 2008-09-30 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Structural basis for the exclusive specificity of Slac2-a/melanophilin for the Rab27 GTPases. Structure, 16, 2008
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3A76
| The crystal structure of LinA | Descriptor: | GLYCEROL, Gamma-hexachlorocyclohexane dehydrochlorinase, SPERMIDINE | Authors: | Okai, M, Kubota, K, Fukuda, M, Nagata, Y, Nagata, K, Tanokura, M. | Deposit date: | 2009-09-15 | Release date: | 2010-09-15 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Crystal structure of g-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26 J.Mol.Biol., 2010
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2E4P
| Crystal structure of BphA3 (oxidized form) | Descriptor: | Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER, SULFATE ION, ... | Authors: | Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T. | Deposit date: | 2006-12-15 | Release date: | 2007-10-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol., 373, 2007
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2E4Q
| Crystal structure of BphA3 (reduced form) | Descriptor: | Biphenyl dioxygenase ferredoxin subunit, FE2/S2 (INORGANIC) CLUSTER | Authors: | Senda, M, Kishigami, S, Kimura, S, Ishida, T, Fukuda, M, Senda, T. | Deposit date: | 2006-12-15 | Release date: | 2007-10-16 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin J.Mol.Biol., 373, 2007
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7C86
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2020-05-28 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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1BOU
| THREE-DIMENSIONAL STRUCTURE OF LIGAB | Descriptor: | 4,5-DIOXYGENASE ALPHA CHAIN, 4,5-DIOXYGENASE BETA CHAIN, FE (III) ION | Authors: | Sugimoto, K, Senda, T, Fukuda, M, Mitsui, Y. | Deposit date: | 1998-08-06 | Release date: | 1999-05-04 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure, 7, 1999
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7E6Z
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E6Y
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E6X
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E70
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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7E71
| Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ... | Authors: | Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O. | Deposit date: | 2021-02-24 | Release date: | 2021-04-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. Elife, 10, 2021
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