7XC1
 
 | | Crystal structure of ERK2 with an allosteric inhibitor 3 | | Descriptor: | (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... | | Authors: | Yoshida, M, Kinoshita, T. | | Deposit date: | 2022-03-22 | | Release date: | 2023-03-22 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Structural basis for ERK2 allosteric inhibitors.
To Be Published
|
|
8YTN
 | | Single-chain Fv antibody of E11 | | Descriptor: | GLYCEROL, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.72 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
|
|
8YTP
 | | Single-chain Fv antibody of E11 complex with NP-glycine under reducing conditions | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, Single-chain Fv antibody of E11 | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.36 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
|
|
8YTO
 | | Single-chain Fv antibody of E11 complex with NP-glycine | | Descriptor: | 2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, GLYCEROL, ... | | Authors: | Yoshida, M, Hanazono, Y, Numoto, N, Ito, N, Oda, M. | | Deposit date: | 2024-03-26 | | Release date: | 2024-07-03 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.04 Å) | | Cite: | Affinity-matured antibody with a disulfide bond in H-CDR3 loop.
Arch.Biochem.Biophys., 758, 2024
|
|
7W5O
 | | Crystal structure of ERK2 with an allosteric inhibitor | | Descriptor: | (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL, 13-[4-({Imidazo[1,2-a]pyridin-2-yl}methoxy)phenyl]-4,8-dioxa-12,14,16,18-tetraazatetracyclo[9.7.0.0^{3,9}.0^{12,17}]octadeca-1(11),2,9,15,17-pentaen-15-amine, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | | Authors: | Yoshida, M, Kinoshita, T. | | Deposit date: | 2021-11-30 | | Release date: | 2022-02-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Identification of a novel target site for ATP-independent ERK2 inhibitors.
Biochem.Biophys.Res.Commun., 593, 2022
|
|
7X4U
 | | Crystal structure of ERK2 with an allosteric inhibitor 2 | | Descriptor: | (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, ... | | Authors: | Yoshida, M, Kinoshita, T. | | Deposit date: | 2022-03-03 | | Release date: | 2023-03-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Structural basis for producing allosteric ERK2 inhibitors
To Be Published
|
|
4V4O
 | | Crystal Structure of the Chaperonin Complex Cpn60/Cpn10/(ADP)7 from Thermus Thermophilus | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DIMETHYL SULFOXIDE, MAGNESIUM ION, ... | | Authors: | Shimamura, T, Koike-Takeshita, A, Yokoyama, K, Masui, R, Murai, N, Yoshida, M, Taguchi, H, Iwata, S. | | Deposit date: | 2004-05-23 | | Release date: | 2014-07-09 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity
STRUCTURE, 12, 2004
|
|
3GQB
 | | Crystal Structure of the A3B3 complex from V-ATPase | | Descriptor: | V-type ATP synthase alpha chain, V-type ATP synthase beta chain | | Authors: | Meher, M, Akimoto, S, Iwata, M, Nagata, K, Hori, Y, Yoshida, M, Yokoyama, S, Iwata, S, Yokoyama, K. | | Deposit date: | 2009-03-24 | | Release date: | 2009-11-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of A(3)B(3) complex of V-ATPase from Thermus thermophilus.
Embo J., 28, 2009
|
|
1VDY
 | | NMR Structure of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana | | Descriptor: | hypothetical protein (RAFL09-17-B18) | | Authors: | Lopez-Mendez, B, Pantoja-Uceda, D, Tomizawa, T, Koshiba, S, Kigawa, T, Shirouzu, M, Terada, T, Inoue, M, Yabuki, T, Aoki, M, Seki, E, Matsuda, T, Hirota, H, Yoshida, M, Tanaka, A, Osanai, T, Seki, M, Shinozaki, K, Yokoyama, S, Guntert, P, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-03-25 | | Release date: | 2005-05-03 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the hypothetical ENTH-VHS domain AT3G16270 from arabidopsis thaliana
To be Published
|
|
1M34
 | | Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate | | Descriptor: | 3-HYDROXY-3-CARBOXY-ADIPIC ACID, ADENOSINE-5'-DIPHOSPHATE, CALCIUM ION, ... | | Authors: | Schmid, B, Einsle, O, Chiu, H.-J, Willing, A, Yoshida, M, Howard, J.B, Rees, D.C. | | Deposit date: | 2002-06-27 | | Release date: | 2003-02-11 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4 Stabilized structure
Biochemistry, 41, 2002
|
|
1M1N
 | | Nitrogenase MoFe protein from Azotobacter vinelandii | | Descriptor: | 3-HYDROXY-3-CARBOXY-ADIPIC ACID, CALCIUM ION, FE(7)-MO-S(9)-N CLUSTER, ... | | Authors: | Einsle, O, Tezcan, F.A, Andrade, S.L.A, Schmid, B, Yoshida, M, Howard, J.B, Rees, D.C. | | Deposit date: | 2002-06-19 | | Release date: | 2002-09-11 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.16 Å) | | Cite: | Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor.
Science, 297, 2002
|
|
1VEG
 | | Solution Structure of RSGI RUH-012, a UBA Domain from Mouse cDNA | | Descriptor: | NEDD8 ultimate buster-1 | | Authors: | Abe, T, Hirota, H, Izumi, K, Yoshida, M, Yamazaki, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-03-31 | | Release date: | 2004-09-30 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of RSGI RUH-012, a UBA Domain from Mouse cDNA
To be Published
|
|
8CAX
 | | Structure of Tau filaments Type II from Subacute Sclerosing Panencephalitis | | Descriptor: | Microtubule-associated protein tau | | Authors: | Qi, C, Hasegawa, M, Takao, M, Sakai, M, Akagi, M, Iwasaki, Y, Yoshida, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2023-01-24 | | Release date: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Identical tau filaments in subacute sclerosing panencephalitis and chronic traumatic encephalopathy.
Acta Neuropathol Commun, 11, 2023
|
|
8CAQ
 | | Structure of Tau filaments Type I from Subacute Sclerosing Panencephalitis | | Descriptor: | Microtubule-associated protein tau | | Authors: | Qi, C, Hasegawa, M, Takao, M, Sakai, M, Akagi, M, Iwasaki, Y, Yoshida, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2023-01-24 | | Release date: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Identical tau filaments in subacute sclerosing panencephalitis and chronic traumatic encephalopathy.
Acta Neuropathol Commun, 11, 2023
|
|
5Y0Z
 | | Human SIRT2 in complex with a specific inhibitor, NPD11033 | | Descriptor: | (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one, NAD-dependent protein deacetylase sirtuin-2, ZINC ION | | Authors: | Kudo, N, Ito, A, Yoshida, M. | | Deposit date: | 2017-07-19 | | Release date: | 2018-07-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2.
Philos. Trans. R. Soc. Lond., B, Biol. Sci., 373, 2018
|
|
6XYO
 | | Multiple system atrophy Type I alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (2.6 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
|
|
6XYP
 | | Multiple system atrophy Type II-1 alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.29 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
|
|
6XYQ
 | | Multiple system atrophy Type II-2 alpha-synuclein filament | | Descriptor: | Alpha-synuclein | | Authors: | Schweighauser, M, Shi, Y, Tarutani, A, Kametani, F, Murzin, A.G, Ghetti, B, Matsubara, T, Tomita, T, Ando, T, Hasegawa, K, Murayama, S, Yoshida, M, Hasegawa, M, Scheres, S.H.W, Goedert, M. | | Deposit date: | 2020-01-30 | | Release date: | 2020-02-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.09 Å) | | Cite: | Structures of alpha-synuclein filaments from multiple system atrophy.
Nature, 585, 2020
|
|
6EII
 | | The crystal structure of CK2alpha in complex with compound 18 | | Descriptor: | (3-chloranyl-4-phenyl-phenyl)methyl-(3-phenylpropyl)azanium, ACETATE ION, Casein kinase II subunit alpha, ... | | Authors: | Brear, P, De Fusco, C, Iegre, J, Yoshida, M, Mitchell, S, Rossmann, M, Carro, L, Sore, H, Hyvonen, M, Spring, D. | | Deposit date: | 2017-09-19 | | Release date: | 2018-02-28 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.935 Å) | | Cite: | Second-generation CK2 alpha inhibitors targeting the alpha D pocket.
Chem Sci, 9, 2018
|
|
6EHK
 | | The crystal structure of CK2alpha in complex with CAM4712 and compound 37 | | Descriptor: | 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[3,5-bis(chloranyl)-4-(2-ethylphenyl)phenyl]methyl]ethanamine, 2-hydroxy-5-methylbenzoic acid, ACETATE ION, ... | | Authors: | Brear, P, De Fusco, C, Iegre, J, Yoshida, M, Mitchell, S, Rossmann, M, Carro, L, Sore, H, Hyvonen, M, Spring, D. | | Deposit date: | 2017-09-13 | | Release date: | 2018-02-28 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Second-generation CK2 alpha inhibitors targeting the alpha D pocket.
Chem Sci, 9, 2018
|
|
6EHU
 | | The crystal structure of CK2alpha in complex with compound 32 | | Descriptor: | 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-(trifluoromethyl)phenyl]methyl]ethanamine, ACETATE ION, Casein kinase II subunit alpha | | Authors: | Brear, P, De Fusco, C, Iegre, J, Yoshida, M, Mitchell, S, Rossmann, M, Carro, L, Sore, H, Hyvonen, M, Spring, D. | | Deposit date: | 2017-09-15 | | Release date: | 2018-02-28 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Second-generation CK2 alpha inhibitors targeting the alpha D pocket.
Chem Sci, 9, 2018
|
|
4XD7
 | | Structure of thermophilic F1-ATPase inhibited by epsilon subunit | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATP synthase epsilon chain, ATP synthase gamma chain, ... | | Authors: | SHIRAKIHARA, Y, SHIRATORI, A, TANIKAWA, H, NAKASAKO, M, YOSHIDA, M, SUZUKI, T. | | Deposit date: | 2014-12-19 | | Release date: | 2015-08-26 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (3.9 Å) | | Cite: | Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.
Febs J., 282, 2015
|
|
4EIW
 | | Whole cytosolic region of atp-dependent metalloprotease FtsH (G399L) | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATP-dependent zinc metalloprotease FtsH | | Authors: | Suno, R, Niwa, H, Tsuchiya, D, Yoshida, M, Morikawa, K. | | Deposit date: | 2012-04-06 | | Release date: | 2012-06-06 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (3.9 Å) | | Cite: | Structure of the whole cytosolic region of ATP-dependent protease FtsH
Mol.Cell, 22, 2006
|
|
4Y6L
 | | Human SIRT2 in complex with myristoylated peptide (H3K9myr) | | Descriptor: | NAD-dependent protein deacetylase sirtuin-2, ZINC ION, peptide THR-ALA-ARG-MYK-SER-THR-GLY | | Authors: | Kudo, N, Ito, A, Yoshida, M. | | Deposit date: | 2015-02-13 | | Release date: | 2016-01-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Biochemistry, 54, 2015
|
|
4Y6Q
 | | Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose | | Descriptor: | NAD-dependent protein deacetylase sirtuin-2, ZINC ION, [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate | | Authors: | Kudo, N, Ito, A, Yoshida, M. | | Deposit date: | 2015-02-13 | | Release date: | 2016-01-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.
Biochemistry, 54, 2015
|
|
