6LKT
 
 | | Crystal structure of the Fab fragment of murine monoclonal antibody KH-1 against Human herpesvirus 6B | | Descriptor: | antibody Fab Fragment L-chain, antibody Fab fragment H chain | | Authors: | Nishimura, M, Novita, B.D, Kato, T, Tjan, L.H, Wang, B, Wakata, A, Poetranto, A.L, Kawabata, A, Tang, H, Aoshi, T, Mori, Y. | | Deposit date: | 2019-12-20 | | Release date: | 2020-06-17 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for the interaction of human herpesvirus 6B tetrameric glycoprotein complex with the cellular receptor, human CD134.
Plos Pathog., 16, 2020
|
|
8IHL
 | | Overlapping tri-nucleosome | | Descriptor: | DNA (353-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Nishimura, M, Fujii, T, Tanaka, H, Maehara, K, Nozawa, K, Takizawa, Y, Ohkawa, Y, Kurumizaka, H. | | Deposit date: | 2023-02-23 | | Release date: | 2024-01-17 | | Last modified: | 2024-01-24 | | Method: | ELECTRON MICROSCOPY (7.64 Å) | | Cite: | Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.
Commun Biol, 7, 2024
|
|
8W5Z
 | | Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of tick anticoagulant protein madanin | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE, ADENOSINE-3'-5'-DIPHOSPHATE, ... | | Authors: | Yoshimura, M, Teramoto, T, Nishimoto, E, Kakuta, Y. | | Deposit date: | 2023-08-28 | | Release date: | 2024-04-10 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal structure of tick tyrosylprotein sulfotransferase reveals the activation mechanism of the tick anticoagulant protein madanin.
J.Biol.Chem., 300, 2024
|
|
2PA2
 | | Crystal structure of human Ribosomal protein L10 core domain | | Descriptor: | 60S ribosomal protein L10, POTASSIUM ION | | Authors: | Nishimura, M, Kaminishi, T, Takemoto, C, Kawazoe, M, Yoshida, T, Tanaka, A, Sugano, S, Shirouzu, M, Ohkubo, T, Yokoyama, S, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-27 | | Release date: | 2008-03-11 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs in Addition to the Conserved Fold
J.Mol.Biol., 377, 2008
|
|
6LTG
 | | Crystal structure of the Fab fragment of murine monoclonal antibody OHV-3 against Human herpesvirus 6B | | Descriptor: | MAGNESIUM ION, antibody Fab fragment H-chain, antibody Fab fragment L-chain | | Authors: | Nishimura, M, Novita, B.D, Kato, T, Tjan, L.H, Wang, B, Wakata, A, Poetranto, A.L, Kawabata, A, Tang, H, Aoshi, T, Mori, Y. | | Deposit date: | 2020-01-22 | | Release date: | 2020-06-17 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.63 Å) | | Cite: | Structural basis for the interaction of human herpesvirus 6B tetrameric glycoprotein complex with the cellular receptor, human CD134.
Plos Pathog., 16, 2020
|
|
5BUN
 | | Crystal structure of an antigenic outer membrane protein ST50 from Salmonella Typhi | | Descriptor: | Outer membrane protein, octyl beta-D-glucopyranoside | | Authors: | Yoshimura, M, Chuankhayan, P, Lin, C.C, Chen, N.C, Yang, M.C, Fun, H.K. | | Deposit date: | 2015-06-04 | | Release date: | 2015-12-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.98 Å) | | Cite: | Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.
Sci Rep, 5, 2015
|
|
7XZZ
 | | Cryo-EM structure of the nucleosome in complex with p53 | | Descriptor: | Cellular tumor antigen p53, DNA (169-MER), Histone H2A type 1-B/E, ... | | Authors: | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-12 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (4.07 Å) | | Cite: | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
|
|
1WKI
 | | solution structure of ribosomal protein L16 from thermus thermophilus HB8 | | Descriptor: | LSU ribosomal protein L16P | | Authors: | Nishimura, M, Yoshida, T, Shirouzu, M, Terada, T, Kuramitsu, S, Yokoyama, S, Ohkubo, T, Kobayashi, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-05-31 | | Release date: | 2004-12-14 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8
J.Mol.Biol., 344, 2004
|
|
7XZX
 | | Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain | | Descriptor: | Cellular tumor antigen p53, DNA (193-MER), Histone H2A type 1-B/E, ... | | Authors: | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-12 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (4.53 Å) | | Cite: | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
|
|
7Y00
 | | Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence | | Descriptor: | DNA (169-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-19 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.96 Å) | | Cite: | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
|
|
7XZY
 | | Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-19 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.97 Å) | | Cite: | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
|
|
7F47
 | | Cryo-EM structure of Rhizobium etli MprF | | Descriptor: | (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate, Hypothetical conserved protein, [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate | | Authors: | Nishimura, M, Hirano, H, Kobayashi, K, Gill, C.P, Phan, C.N.K, Kise, Y, Kusakizako, T, Yamashita, K, Ito, Y, Roy, H, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-06-17 | | Release date: | 2022-06-22 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (2.99 Å) | | Cite: | Cryo-EM structure of Rhizobium etli MprF
To Be Published
|
|
5WX8
 | | Human herpesvirus 6A immediate early protein 2 C-terminal domain | | Descriptor: | Immediate-early protein 2 | | Authors: | Nishimura, M, Wang, J, Wakata, A, Sakamoto, K, Mori, Y. | | Deposit date: | 2017-01-06 | | Release date: | 2017-08-02 | | Last modified: | 2017-12-06 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of the DNA-Binding Domain of Human Herpesvirus 6A Immediate Early Protein 2.
J. Virol., 91, 2017
|
|
3ABN
 | | Crystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.02 A | | Descriptor: | collagen-like peptide | | Authors: | Okuyama, K, Shimura, M, Kawaguchi, T, Noguchi, K, Mizuno, K, Bachinger, H.P. | | Deposit date: | 2009-12-16 | | Release date: | 2010-12-01 | | Last modified: | 2013-11-27 | | Method: | X-RAY DIFFRACTION (1.02 Å) | | Cite: | Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 angstrom resolution.
Biopolymers, 99, 2013
|
|
4V60
 | | The structure of rat liver vault at 3.5 angstrom resolution | | Descriptor: | Major vault protein | | Authors: | Kato, K, Zhou, Y, Tanaka, H, Yao, M, Yamashita, E, Yoshimura, M, Tsukihara, T. | | Deposit date: | 2008-10-24 | | Release date: | 2014-07-09 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | The structure of rat liver vault at 3.5 angstrom resolution
Science, 323, 2009
|
|
7YV1
 | | Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Isoform 2B of GTPase KRas, KA30L Fab H-chain, ... | | Authors: | Irie, M, Fukami, T.A, Matsuo, A, Saka, K, Nishimura, M, Saito, H, Torizawa, T, Tanada, M, Ohta, A. | | Deposit date: | 2022-08-18 | | Release date: | 2023-07-26 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.454 Å) | | Cite: | Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets.
J.Am.Chem.Soc., 145, 2023
|
|
4WIZ
 | | Crystal structure of Grouper nervous necrosis virus-like particle at 3.6A | | Descriptor: | CALCIUM ION, Coat protein | | Authors: | Chen, N.C, Chen, C.J, Yoshimura, M, Guan, H.H, Chen, T.Y. | | Deposit date: | 2014-09-28 | | Release date: | 2015-10-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Plos Pathog., 11, 2015
|
|
8H3M
 | | Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy chain, Spike glycoprotein | | Authors: | Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y. | | Deposit date: | 2022-10-09 | | Release date: | 2023-05-10 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
|
|
8H3N
 | | Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy-chain, MO1 light chain, ... | | Authors: | Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y. | | Deposit date: | 2022-10-09 | | Release date: | 2023-05-10 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (2.73 Å) | | Cite: | Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
|
|
8XI6
 | | SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Ishimaru, H, Nishimura, M, Shigematsu, H, Marini, M.I, Hasegawa, N, Takamiya, R, Iwata, S, Mori, Y. | | Deposit date: | 2023-12-19 | | Release date: | 2024-04-24 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein.
J.Virol., 98, 2024
|
|
4RFT
 | | T=1 subviral particle of Grouper nervous necrosis virus capsid protein deletion mutant (delta 1-34 & 218-338) | | Descriptor: | Coat protein | | Authors: | Chen, N.C, Chen, C.J, Yoshimura, M, Guan, H.H, Chen, T.Y. | | Deposit date: | 2014-09-27 | | Release date: | 2015-10-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Plos Pathog., 11, 2015
|
|
5T09
 | | The structure of the type III effector HopBA1 | | Descriptor: | CHLORIDE ION, POTASSIUM ION, Type III secretion system effector HopBA1 | | Authors: | Cherkis, K, Machius, M, Nishimura, M.T, Dangl, J.L. | | Deposit date: | 2016-08-15 | | Release date: | 2017-02-01 | | Last modified: | 2019-11-20 | | Method: | X-RAY DIFFRACTION (2.013 Å) | | Cite: | TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
|
|
4RFU
 | | Crystal structure of truncated P-domain from Grouper nervous necrosis virus capsid protein at 1.2A | | Descriptor: | CALCIUM ION, Coat protein, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Chen, N.C, Chen, C.J, Yoshimura, M, Guan, H.H, Chen, T.Y. | | Deposit date: | 2014-09-27 | | Release date: | 2015-10-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.2 Å) | | Cite: | Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Plos Pathog., 11, 2015
|
|
6AB6
 | | Cryo-EM structure of T=3 Penaeus vannamei nodavirus | | Descriptor: | CALCIUM ION, Capsid protein | | Authors: | Chen, N.C, Miyazaki, N, Yoshimura, M, Guan, H.H, Lin, C.C, Iwasaki, K, Chen, C.J. | | Deposit date: | 2018-07-20 | | Release date: | 2019-03-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Commun Biol, 2, 2019
|
|
5AWL
 | | CRYSTAL STRUCTURE OF A MUTANT OF CHIGNOLIN, CLN025 | | Descriptor: | A mutant of Chignolin, CLN025 | | Authors: | Akiba, T, Ishimura, M, Odahara, T, Harata, K, Honda, S. | | Deposit date: | 2015-07-05 | | Release date: | 2015-08-12 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.11 Å) | | Cite: | Crystal structure of a ten-amino acid protein
J.Am.Chem.Soc., 130, 2008
|
|
