8HSH
| Thermus thermophilus RNA polymerase coreenzyme | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | Authors: | Murayama, Y, Ehara, H, Sekine, S. | Deposit date: | 2022-12-19 | Release date: | 2023-05-03 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv, 9, 2023
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8HSG
| Thermus thermophilus RNA polymerase elongation complex | Descriptor: | DNA (27-MER), DNA (37-MER), DNA-directed RNA polymerase subunit alpha, ... | Authors: | Murayama, Y, Ehara, H, Sekine, S. | Deposit date: | 2022-12-19 | Release date: | 2023-05-03 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv, 9, 2023
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8HSL
| Thermus thermophilus RNA polymerase bound with an inverted Rho hexamer | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, DNA-directed RNA polymerase subunit alpha, ... | Authors: | Murayama, Y, Ehara, H, Sekine, S. | Deposit date: | 2022-12-19 | Release date: | 2023-05-03 | Method: | ELECTRON MICROSCOPY (5.8 Å) | Cite: | Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv, 9, 2023
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8HSJ
| Thermus thermophilus transcription termination factor Rho bound with ADP-BeF3 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, MAGNESIUM ION, ... | Authors: | Murayama, Y, Ehara, H, Sekine, S. | Deposit date: | 2022-12-19 | Release date: | 2023-05-03 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv, 9, 2023
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8HSR
| Thermus thermophilus Rho-engaged RNAP elongation complex | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, DNA (31-MER), ... | Authors: | Murayama, Y, Ehara, H, Sekine, S. | Deposit date: | 2022-12-20 | Release date: | 2023-05-03 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci Adv, 9, 2023
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5Z85
| The structure of azide-bound cytochrome c oxidase determined using the another batch crystals exposed to 20 mM azide solution for 2 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-01-31 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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5Z84
| The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-01-31 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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5ZCP
| azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 2 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-02-19 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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5Z86
| azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 3 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-01-31 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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5ZCQ
| Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10 mM azide solution for 2 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-02-19 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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5ZCO
| azide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 mM azide solution for 2 days | 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: | Shimada, A, Hatano, K, Tadehara, H, Tsukihara, T. | Deposit date: | 2018-02-19 | Release date: | 2018-08-15 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity. J. Biol. Chem., 293, 2018
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8KB5
| Cryo-EM structure of the human nucleosome containing H3.8 | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Hirai, H, Kujirai, T, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-08-03 | Release date: | 2023-10-18 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.26133 Å) | Cite: | Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8. J.Biochem., 174, 2023
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8JL9
| Cryo-EM structure of the human nucleosome with scFv | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2023-11-08 | Method: | ELECTRON MICROSCOPY (2.65 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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8JLD
| Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2023-11-15 | Method: | ELECTRON MICROSCOPY (2.48 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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8JLB
| Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2023-11-08 | Method: | ELECTRON MICROSCOPY (2.36 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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8JLA
| Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-06-02 | Release date: | 2023-10-04 | Last modified: | 2023-11-08 | Method: | ELECTRON MICROSCOPY (3.44 Å) | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res., 51, 2023
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7WLR
| Cryo-EM structure of the nucleosome containing Komagataella pastoris histones | Descriptor: | DNA (145-MER), Histone H2A, Histone H2B, ... | Authors: | Fukushima, Y, Hatazawa, S, Hirai, S, Kujirai, T, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2022-01-13 | Release date: | 2022-07-13 | Last modified: | 2022-08-10 | Method: | ELECTRON MICROSCOPY (3.54 Å) | Cite: | Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones. J.Biochem., 172, 2022
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7VGU
| Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion | Descriptor: | BROMIDE ION, Chloride pumping rhodopsin, DECANE, ... | Authors: | Hosaka, T, Nango, E, Nakane, T, Luo, F, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2021-09-18 | Release date: | 2022-02-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc.Natl.Acad.Sci.USA, 119, 2022
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7VGT
| Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3: resting state structure with bromide ion | Descriptor: | BROMIDE ION, Chloride pumping rhodopsin, DECANE, ... | Authors: | Hosaka, T, Nango, E, Nakane, T, Luo, F, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2021-09-18 | Release date: | 2022-02-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc.Natl.Acad.Sci.USA, 119, 2022
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7VGV
| Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA | Descriptor: | CHLORIDE ION, Chloride pumping rhodopsin, HEXADECANE, ... | Authors: | Hosaka, T, Nango, E, Nakane, T, Luo, F, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2021-09-18 | Release date: | 2022-02-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc.Natl.Acad.Sci.USA, 119, 2022
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8GVM
| The structure of azide-bound cytochrome C oxidase determined using the crystals exposed to 20 mm azide solution for 4 days | 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, Shimada, A. | Deposit date: | 2022-09-15 | Release date: | 2022-10-19 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.851 Å) | Cite: | X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity J. Biol. Chem., 293, 2018
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