5B1B
 
 | | Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution | | 分子名称: | (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, ... | | 著者 | Yano, N, Muramoto, K, Shimada, A, Takemura, S, Baba, J, Fujisawa, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | 登録日 | 2015-12-01 | | 公開日 | 2016-09-14 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
J.Biol.Chem., 291, 2016
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5B1A
 | | Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution | | 分子名称: | (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, ... | | 著者 | Yano, N, Muramoto, K, Shimada, A, Takemura, S, Baba, J, Fujisawa, H, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | 登録日 | 2015-12-01 | | 公開日 | 2016-09-14 | | 最終更新日 | 2020-02-26 | | 実験手法 | X-RAY DIFFRACTION (1.5 Å) | | 主引用文献 | The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
J.Biol.Chem., 291, 2016
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7YQS
 | | Neutron structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex | | 分子名称: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, CALCIUM ION, ... | | 著者 | Yano, N, Kondo, T, Kusaka, K, Yamada, T, Arakawa, T, Sakamoto, T, Fushinobu, S. | | 登録日 | 2022-08-08 | | 公開日 | 2023-08-09 | | 最終更新日 | 2024-03-27 | | 実験手法 | NEUTRON DIFFRACTION (1.25 Å), X-RAY DIFFRACTION | | 主引用文献 | 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., 300, 2024
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8I4D
 | | X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex at 100K | | 分子名称: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, CALCIUM ION, ... | | 著者 | Yano, N, Kondo, T, Kusaka, K, Yamada, T, Arakawa, T, Sakamoto, T, Fushinobu, S. | | 登録日 | 2023-01-19 | | 公開日 | 2024-01-24 | | 最終更新日 | 2024-03-27 | | 実験手法 | X-RAY DIFFRACTION (1.06 Å) | | 主引用文献 | 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., 300, 2024
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3X2Q
 | | X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution | | 分子名称: | (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, ... | | 著者 | Yano, N, Muramoto, K, Mochizuki, M, Shinzawa-Itoh, K, Yamashita, E, Yoshikawa, S, Tsukihara, T. | | 登録日 | 2014-12-26 | | 公開日 | 2015-06-10 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution.
Acta Crystallogr F Struct Biol Commun, 71, 2015
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4V2T
 | | Membrane embedded pleurotolysin pore with 13 fold symmetry | | 分子名称: | PLEUROTOLYSIN A, PLEUROTOLYSIN B | | 著者 | Lukoyanova, N, Kondos, S.C, Farabella, I, Law, R.H.P, Reboul, C.F, Caradoc-Davies, T.T, Spicer, B.A, Kleifeld, O, Perugini, M, Ekkel, S, Hatfaludi, T, Oliver, K, Hotze, E.M, Tweten, R.K, Whisstock, J.C, Topf, M, Dunstone, M.A, Saibil, H.R. | | 登録日 | 2014-10-15 | | 公開日 | 2015-02-18 | | 最終更新日 | 2017-08-30 | | 実験手法 | ELECTRON MICROSCOPY (11 Å) | | 主引用文献 | Conformational Changes During Pore Formation by the Perforin-Related Protein Pleurotolysin.
Plos Biol., 13, 2015
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4V3A
 | | Membrane bound pleurotolysin prepore (TMH1 lock) trapped with engineered disulphide cross-link | | 分子名称: | PLEUROTOLYSIN A, PLEUROTOLYSIN B | | 著者 | Lukoyanova, N, Kondos, S.C, Farabella, I, Law, R.H.P, Reboul, C.F, CaradocDavies, T.T, Spicer, B.A, Kleifeld, O, Perugini, M, Ekkel, S, Hatfaludi, T, Oliver, K, Hotze, E.M, Tweten, R.K, Whisstock, J.C, Topf, M, Dunstone, M.A, Saibil, H.R. | | 登録日 | 2014-10-17 | | 公開日 | 2015-02-18 | | 最終更新日 | 2017-08-30 | | 実験手法 | ELECTRON MICROSCOPY (15 Å) | | 主引用文献 | Conformational Changes During Pore Formation by the Perforin-Related Protein Pleurotolysin.
Plos Biol., 13, 2015
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4V3M
 | | Membrane bound pleurotolysin prepore (TMH2 helix lock) trapped with engineered disulphide cross-link | | 分子名称: | PLEUROTOLYSIN A, PLEUROTOLYSIN B | | 著者 | Lukoyanova, N, Kondos, S.C, Farabella, I, Law, R.H.P, Reboul, C.F, Caradoc-Davies, T.T, Spicer, B.A, Kleifeld, O, Perugini, M, Ekkel, S, Hatfaludi, T, Oliver, K, Hotze, E.M, Tweten, R.K, Whisstock, J.C, Topf, M, Dunstone, M.A, Saibil, H.R. | | 登録日 | 2014-10-20 | | 公開日 | 2015-02-18 | | 最終更新日 | 2017-08-23 | | 実験手法 | ELECTRON MICROSCOPY (17 Å) | | 主引用文献 | Conformational Changes During Pore Formation by the Perforin-Related Protein Pleurotolysin.
Plos Biol., 13, 2015
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4V3N
 | | Membrane bound pleurotolysin prepore (TMH2 strand lock) trapped with engineered disulphide cross-link | | 分子名称: | PLEUROTOLYSIN A, PLEUROTOLYSIN B | | 著者 | Lukoyanova, N, Kondos, S.C, Farabella, I, Law, R.H.P, Reboul, C.F, Caradoc-Davies, T.T, Spicer, B.A, Kleifeld, O, Perugini, M, Ekkel, S, Hatfaludi, T, Oliver, K, Hotze, E.M, Tweten, R.K, Whisstock, J.C, Topf, M, Dunstone, M.A, Saibil, H.R. | | 登録日 | 2014-10-20 | | 公開日 | 2015-02-18 | | 最終更新日 | 2017-08-23 | | 実験手法 | ELECTRON MICROSCOPY (14 Å) | | 主引用文献 | Conformational Changes During Pore Formation by the Perforin-Related Protein Pleurotolysin.
Plos Biol., 13, 2015
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3A4O
 | | Lyn kinase domain | | 分子名称: | STAUROSPORINE, Tyrosine-protein kinase Lyn | | 著者 | Miyano, N, Kinoshita, T, Tada, T. | | 登録日 | 2009-07-11 | | 公開日 | 2009-12-08 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (3 Å) | | 主引用文献 | Structural basis for the inhibitor recognition of human Lyn kinase domain
Bioorg.Med.Chem.Lett., 19, 2009
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6L9C
 | | Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 | | 分子名称: | COPPER (II) ION, Phenylethylamine oxidase, SODIUM ION | | 著者 | 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, Y, Tanizawa, K, Adachi, M, Okajima, T. | | 登録日 | 2019-11-08 | | 公開日 | 2020-04-29 | | 最終更新日 | 2023-11-22 | | 実験手法 | NEUTRON DIFFRACTION (1.14 Å), X-RAY DIFFRACTION | | 主引用文献 | Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.
Proc.Natl.Acad.Sci.USA, 117, 2020
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3ASO
 | | Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength | | 分子名称: | (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, ... | | 著者 | Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | 登録日 | 2010-12-17 | | 公開日 | 2011-08-03 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
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3ASN
 | | Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength | | 分子名称: | (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, ... | | 著者 | Suga, M, Yano, N, Muramoto, K, Shinzawa-Itoh, K, Maeda, T, Yamashita, E, Tsukihara, T, Yoshikawa, S. | | 登録日 | 2010-12-17 | | 公開日 | 2011-08-03 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (3 Å) | | 主引用文献 | Distinguishing between Cl- and O2(2-) as the bridging element between Fe3+ and Cu2+ in resting-oxidized cytochrome c oxidase
Acta Crystallogr.,Sect.D, 67, 2011
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6KK8
 | | XN joint refinement of manganese catalase from Thermus Thermophilus HB27 | | 分子名称: | 1,2-ETHANEDIOL, MANGANESE (III) ION, OXYGEN ATOM, ... | | 著者 | Yamada, T, Yano, N, Kusaka, K. | | 登録日 | 2019-07-24 | | 公開日 | 2019-09-04 | | 最終更新日 | 2024-04-03 | | 実験手法 | NEUTRON DIFFRACTION (1.37 Å), X-RAY DIFFRACTION | | 主引用文献 | Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27
J.Appl.Crystallogr., 2019
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3WG7
 | | A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography | | 分子名称: | (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, ... | | 著者 | 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. | | 登録日 | 2013-07-29 | | 公開日 | 2014-04-30 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.
Nat.Methods, 11, 2014
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8B6U
 | | Mpf2Ba1 monomer | | 分子名称: | MAGNESIUM ION, Mpf2Ba1 | | 著者 | Marini, G, Poland, B, Leininger, C, Lukoyanova, N, Spielbauer, D, Barry, J, Altier, D, Lum, A, Scolaro, E, Perez-Ortega, C, Yalpani, N, Sandahl, G, Mabry, T, Klever, J, Nowatzki, T, Zhao, J.Z, Sethi, A, Kassa, A, Crane, V, Lu, A, Nelson, M.E, Eswar, N, Topf, M, Saibil, H.R. | | 登録日 | 2022-09-27 | | 公開日 | 2023-05-31 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (2.134 Å) | | 主引用文献 | Structural journey of an insecticidal protein against western corn rootworm.
Nat Commun, 14, 2023
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8B6W
 | | Mpf2Ba1 pore | | 分子名称: | MAGNESIUM ION, Mpf2Ba1 | | 著者 | Marini, G, Poland, B, Leininger, C, Lukoyanova, N, Spielbauer, D, Barry, J, Altier, D, Lum, A, Scolaro, E, Perez Ortega, C, Yalpani, N, Sandahl, G, Mabry, T, Klever, J, Nowatzki, T, Zhao, J.Z, Sethi, A, Kassa, A, Crane, V, Lu, A, Nelson, M.E, Eswar, N, Topf, M, Saibil, H.R. | | 登録日 | 2022-09-27 | | 公開日 | 2023-05-31 | | 最終更新日 | 2023-07-26 | | 実験手法 | ELECTRON MICROSCOPY (2.6 Å) | | 主引用文献 | Structural journey of an insecticidal protein against western corn rootworm.
Nat Commun, 14, 2023
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8B6V
 | | Mp2Ba1 pre-pore | | 分子名称: | MAGNESIUM ION, Mpf2Ba1 | | 著者 | Marini, G, Poland, B, Leininger, C, Lukoyanova, N, Spielbauer, D, Barry, J, Altier, D, Lum, A, Scolaro, E, Perez Ortega, C, Yalpani, N, Sandahl, G, Mabry, T, Klever, J, Nowatzki, T, Zhao, J.Z, Sethi, A, Kassa, A, Crane, V, Lu, A, Nelson, M.E, Eswar, N, Topf, M, Saibil, H.R. | | 登録日 | 2022-09-27 | | 公開日 | 2023-05-31 | | 最終更新日 | 2023-07-26 | | 実験手法 | ELECTRON MICROSCOPY (3.1 Å) | | 主引用文献 | Structural journey of an insecticidal protein against western corn rootworm.
Nat Commun, 14, 2023
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7O43
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7O3J
 | | O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwE protein, TrwF protein, TrwH protein | | 著者 | Mace, K, Vadakkepat, A.K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-04-01 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (2.6 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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7OIU
 | | Inner Membrane Complex (IMC) protomer structure (TrwM/VirB3, TrwK/VirB4, TrwG/VirB8tails) from the fully-assembled R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwG protein, TrwK protein, TrwM protein | | 著者 | Mace, K, Vadakkepat, A.K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-05-12 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (3.7 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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7O3V
 | | Stalk complex structure (TrwJ/VirB5-TrwI/VirB6) from the fully-assembled R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwI protein, TrwJ protein | | 著者 | Mace, K, Vadakkepat, A.K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-04-03 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (3.7 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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7O3T
 | | I-layer structure (TrwF/VirB9NTD, TrwE/VirB10NTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwE protein, TrwF protein | | 著者 | Mace, K, Vadakkepat, A.K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-04-03 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (3.1 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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7O41
 | | Hexameric composite model of the Inner Membrane Complex (IMC) with the Arches from the fully-assembled R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwG protein, TrwK protein, TrwM protein | | 著者 | Mace, K, Vadakkepat, A.K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-04-04 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (7.6 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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7O42
 | | TrwK/VirB4unbound trimer of dimers complex (with Hcp1) from the R388 type IV secretion system determined by cryo-EM. | | 分子名称: | TrwK protein,Protein hcp1 | | 著者 | Vadakkepat, A.K, Mace, K, Lukoyanova, N, Waksman, G. | | 登録日 | 2021-04-04 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-07-20 | | 実験手法 | ELECTRON MICROSCOPY (4.1 Å) | | 主引用文献 | Cryo-EM structure of a type IV secretion system.
Nature, 607, 2022
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