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PDB: 248 件

7CJ3
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Crystal structure of the transmembrane domain of Salpingoeca rosetta rhodopsin phosphodiesterase
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL
著者Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
登録日2020-07-09
公開日2020-11-25
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
7D7Q
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Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Phosphodiesterase, RETINAL
著者Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
登録日2020-10-05
公開日2020-11-18
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (3.5 Å)
主引用文献Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
7D7P
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Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase
分子名称: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, ...
著者Ikuta, T, Shihoya, W, Yamashita, K, Nureki, O.
登録日2020-10-05
公開日2020-11-18
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structural insights into the mechanism of rhodopsin phosphodiesterase.
Nat Commun, 11, 2020
7DH5
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Dog beta3 adrenergic receptor bound to mirabegron in complex with a miniGs heterotrimer
分子名称: 2-(2-azanyl-1,3-thiazol-4-yl)-N-[4-[2-[[(2R)-2-oxidanyl-2-phenyl-ethyl]amino]ethyl]phenyl]ethanamide, Beta-3 adrenergic receptor, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, ...
著者Shihoya, W, Yamashita, K, Nureki, O.
登録日2020-11-12
公開日2021-08-04
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Cryo-EM structure of the beta 3-adrenergic receptor reveals the molecular basis of subtype selectivity.
Mol.Cell, 81, 2021
7DVO
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Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL
分子名称: GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ...
著者Nomura, T, Kimura, T, Kanematsu, Y, Yamashita, K, Hirata, K, Ueno, G, Murakami, H, Hisano, T, Yamagiwa, R, Takeda, H, Gopalasingam, C, Yuki, K, Kousaka, R, Yanagasawa, S, Shoji, O, Kumasaka, T, Takano, Y, Ago, H, Yamamoto, M, Sugimoto, H, Tosha, T, Kubo, M, Shiro, Y.
登録日2021-01-14
公開日2021-05-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.
Proc.Natl.Acad.Sci.USA, 118, 2021
7CCS
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Consensus mutated xCT-CD98hc complex
分子名称: 4F2 cell-surface antigen heavy chain, Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System
著者Oda, K, Lee, Y, Takemoto, M, Yamashita, K, Nishizawa, T, Nureki, O.
登録日2020-06-17
公開日2020-12-09
最終更新日2020-12-16
実験手法ELECTRON MICROSCOPY (6.2 Å)
主引用文献Consensus mutagenesis approach improves the thermal stability of system x c - transporter, xCT, and enables cryo-EM analyses.
Protein Sci., 29, 2020
7C7L
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Cryo-EM structure of the Cas12f1-sgRNA-target DNA complex
分子名称: CRISPR-associated protein Cas14a.1, DNA (40-mer), ZINC ION, ...
著者Takeda, N.S, Nakagawa, R, Okazaki, S, Hirano, H, Kobayashi, K, Kusakizako, T, Nishizawa, T, Yamashita, K, Nishimasu, H, Nureki, O.
登録日2020-05-26
公開日2020-12-23
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structure of the miniature type V-F CRISPR-Cas effector enzyme.
Mol.Cell, 81, 2021
8P3W
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Homomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 4
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate, Glutamate receptor 1 flip isoform, ...
著者Zhang, D, Krieger, J.M, Yamashita, K, Greger, I.
登録日2023-05-18
公開日2023-08-30
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.53 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3X
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Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 1
分子名称: Glutamate receptor 2, Voltage-dependent calcium channel gamma-2 subunit
著者Krieger, J.M, Zhang, D, Yamashita, K, Greger, I.H.
登録日2023-05-18
公開日2023-08-30
最終更新日2023-10-11
実験手法ELECTRON MICROSCOPY (3.36 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3S
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Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 2
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate, Glutamate receptor 2, ...
著者Zhang, D, Krieger, J.M, Yamashita, K, Greger, I.
登録日2023-05-18
公開日2023-08-30
最終更新日2023-10-11
実験手法ELECTRON MICROSCOPY (2.95 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3Q
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Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 3
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate, Glutamate receptor 2, ...
著者Zhang, D, Krieger, J.M, Yamashita, K, Greger, I.
登録日2023-05-18
公開日2023-08-30
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.95 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3Z
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BU of 8p3z by Molmil
Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 2
分子名称: Glutamate receptor 2, Voltage-dependent calcium channel gamma-2 subunit
著者Krieger, J.M, Zhang, D, Yamashita, K, Greger, I.H.
登録日2023-05-18
公開日2023-08-30
最終更新日2023-10-11
実験手法ELECTRON MICROSCOPY (3.46 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3Y
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Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 3
分子名称: Glutamate receptor 2, Voltage-dependent calcium channel gamma-2 subunit
著者Krieger, J.M, Zhang, D, Yamashita, K, Greger, I.H.
登録日2023-05-18
公開日2023-08-30
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.55 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8PIV
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BU of 8piv by Molmil
Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 1
分子名称: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate, Glutamate receptor, ...
著者Zhang, D, Krieger, J.M, Yamashita, K, Greger, I.H.
登録日2023-06-22
公開日2023-08-30
最終更新日2023-10-11
実験手法ELECTRON MICROSCOPY (3.46 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3V
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Homomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 3
分子名称: Glutamate receptor 1 flip isoform, Voltage-dependent calcium channel gamma-3 subunit
著者Zhang, D, Krieger, J.M, Yamashita, K, Greger, I.H.
登録日2023-05-18
公開日2023-08-30
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.53 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
8P3T
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BU of 8p3t by Molmil
Homomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 1
分子名称: Glutamate receptor 1 flip isoform, Voltage-dependent calcium channel gamma-3 subunit
著者Zhang, D, Krieger, J, Yamashita, K, Greger, I.
登録日2023-05-18
公開日2023-08-30
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.39 Å)
主引用文献Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Nature, 621, 2023
7E3G
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Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant in the living cell
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T.
登録日2021-02-08
公開日2021-12-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.86 Å)
主引用文献Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament.
Angew.Chem.Int.Ed.Engl., 60, 2021
7E3E
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Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T.
登録日2021-02-08
公開日2021-12-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament.
Angew.Chem.Int.Ed.Engl., 60, 2021
7E3F
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Crystal structure of Trypanosoma brucei cathepsin B Y217C/S275C mutant
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Cysteine peptidase C (CPC), beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
著者Abe, S, Pham, T.T, Negishi, H, Yamashita, K, Hirata, K, Ueno, T.
登録日2021-02-08
公開日2021-12-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament.
Angew.Chem.Int.Ed.Engl., 60, 2021
7EK2
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Cryo-EM structure of VCCN1 in lipid nanodisc
分子名称: Bestrophin-like protein
著者Hagino, T, Kato, T, Kasuya, G, Kobayashi, K, Kusakizako, T, Yamashita, K, Nishizawa, T, Nureki, O.
登録日2021-04-03
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Cryo-EM structures of thylakoid-located voltage-dependent chloride channel VCCN1.
Nat Commun, 13, 2022
7EK1
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Cryo-EM structure of VCCN1 in detergent
分子名称: Bestrophin-like protein
著者Hagino, T, Kato, T, Kasuya, G, Kobayashi, K, Kusakizako, T, Yamashita, K, Nishizawa, T, Nureki, O.
登録日2021-04-03
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Cryo-EM structures of thylakoid-located voltage-dependent chloride channel VCCN1.
Nat Commun, 13, 2022
7EK3
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Cryo-EM structure of VCCN1 Y332A mutant in lipid nanodisc
分子名称: Bestrophin-like protein
著者Hagino, T, Kato, T, Kasuya, G, Kobayashi, K, Kusakizako, T, Yamashita, K, Nishizawa, T, Nureki, O.
登録日2021-04-03
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Cryo-EM structures of thylakoid-located voltage-dependent chloride channel VCCN1.
Nat Commun, 13, 2022
3A6J
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E122Q mutant creatininase complexed with creatine
分子名称: Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-09-02
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6D
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Creatininase complexed with 1-methylguanidine
分子名称: 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ...
著者Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
登録日2009-08-31
公開日2010-02-09
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3WSU
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Crystal structure of beta-mannanase from Streptomyces thermolilacinus
分子名称: Beta-mannanase, GLYCEROL, SODIUM ION
著者Kumagai, Y, Yamashita, K, Okuyama, M, Hatanaka, T, Yao, M, Kimura, A.
登録日2014-03-26
公開日2015-05-20
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition
Febs J., 282, 2015

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