3B0F
| Crystal structure of the UBA domain of p62 and its interaction with ubiquitin | Descriptor: | SULFATE ION, Sequestosome-1 | Authors: | Isogai, S, Morimoto, D, Arita, K, Unzai, S, Tenno, T, Hasegawa, J, Sou, Y, Komatsu, M, Tanaka, K, Shirakawa, M, Tochio, H. | Deposit date: | 2011-06-09 | Release date: | 2011-06-29 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Crystal structure of the ubiquitin-associated (UBA) domain of p62 and its interaction with ubiquitin. J.Biol.Chem., 286, 2011
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2ZKD
| Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3'), ... | Authors: | Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M. | Deposit date: | 2008-03-19 | Release date: | 2008-09-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism Nature, 455, 2008
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3ATQ
| Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius | Descriptor: | Conserved Archaeal protein, DIHYDROFLAVINE-ADENINE DINUCLEOTIDE, TETRADECANE | Authors: | Sasaki, D, Fujihashi, M, Murakami, M, Yoshimura, T, Hemmi, H, Miki, K. | Deposit date: | 2011-01-12 | Release date: | 2011-05-04 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structure and mutation analysis of archaeal geranylgeranyl reductase J.Mol.Biol., 409, 2011
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2EI9
| Crystal structure of R1Bm endonuclease domain | Descriptor: | ACETIC ACID, Non-LTR retrotransposon R1Bmks ORF2 protein | Authors: | Maita, N, Aoyagi, H, Osanai, M, Shirakawa, M, Fujiwara, H. | Deposit date: | 2007-03-12 | Release date: | 2007-07-17 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. Nucleic Acids Res., 35, 2007
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7D8K
| Solution structure of the methyl-CpG binding domain of MBD6 from Arabidopsis thaliana | Descriptor: | Methyl-CpG-binding domain-containing protein 6 | Authors: | Mahana, Y, Ohki, I, Walinda, E, Morimoto, D, Sugase, K, Shirakawa, M. | Deposit date: | 2020-10-08 | Release date: | 2021-10-20 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Structural Insights into Methylated DNA Recognition by the Methyl-CpG Binding Domain of MBD6 from Arabidopsis thaliana . Acs Omega, 7, 2022
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7CJV
| Solution structure of monomeric superoxide dismutase 1 with an additional mutation H46W in a dilute environment | Descriptor: | Monomeric Human Cu,Zn Superoxide dismutase | Authors: | Iwakawa, N, Morimoto, D, Walinda, E, Danielsson, J, Shirakawa, M, Sugase, K. | Deposit date: | 2020-07-14 | Release date: | 2021-05-26 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 beta-Barrel. J.Phys.Chem.B, 125, 2021
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2ZKG
| Crystal structure of unliganded SRA domain of mouse Np95 | Descriptor: | 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase UHRF1 | Authors: | Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M. | Deposit date: | 2008-03-19 | Release date: | 2008-09-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.77 Å) | Cite: | Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism Nature, 455, 2008
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7CJW
| Solution structure of monomeric superoxide dismutase 1 with an additional mutation H46W in a crowded environment | Descriptor: | Monomeric Human Cu,Zn Superoxide dismutase | Authors: | Iwakawa, N, Morimoto, D, Walinda, E, Danielsson, J, Shirakawa, M, Sugase, K. | Deposit date: | 2020-07-14 | Release date: | 2021-05-26 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 beta-Barrel. J.Phys.Chem.B, 125, 2021
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2ZKF
| Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA | Descriptor: | DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)-3'), DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)-3'), E3 ubiquitin-protein ligase UHRF1 | Authors: | Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M. | Deposit date: | 2008-03-19 | Release date: | 2008-09-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism Nature, 455, 2008
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3A4R
| The crystal structure of SUMO-like domain 2 in Nip45 | Descriptor: | 1,2-ETHANEDIOL, NFATC2-interacting protein, SULFATE ION | Authors: | Sekiyama, N, Arita, K, Ikeda, Y, Ariyoshi, M, Tochio, H, Saitoh, H, Shirakawa, M. | Deposit date: | 2009-07-14 | Release date: | 2010-02-02 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1 Å) | Cite: | Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45 Proteins, 78, 2009
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3A1A
| Crystal Structure of the DNMT3A ADD domain | Descriptor: | 1,2-ETHANEDIOL, DNA (cytosine-5)-methyltransferase 3A, ZINC ION | Authors: | Otani, J, Arita, K, Ariyoshi, M, Shirakawa, M. | Deposit date: | 2009-03-28 | Release date: | 2009-11-10 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain Embo Rep., 10, 2009
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2RPA
| The solution structure of N-terminal domain of microtubule severing enzyme | Descriptor: | Katanin p60 ATPase-containing subunit A1 | Authors: | Iwaya, N, Kuwahara, Y, Unzai, S, Nagata, T, Tomii, K, Goda, N, Tochio, H, Shirakawa, M, Hiroaki, H. | Deposit date: | 2008-05-13 | Release date: | 2009-05-26 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | A common substrate recognition mode conserved between katanin P60 and VPS4 governs microtubule severing and membrane skeleton reorganization J.Biol.Chem., 285, 2010
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2MX2
| UBX-L domain of VCIP135 | Descriptor: | Deubiquitinating protein VCIP135 | Authors: | Iwazu, T, Murayama, S, Igarashi, R, Hrioaki, H, Shirakawa, M, Tochio, H. | Deposit date: | 2014-12-07 | Release date: | 2016-07-13 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Structure and interaction mode of the UBX-L domain of VCIP135 determined by solution NMR spectroscopy To be Published
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1IXF
| Crystal Structure of the K intermediate of bacteriorhodopsin | Descriptor: | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, RETINAL, ... | Authors: | Matsui, Y, Sakai, K, Murakami, M, Shiro, Y, Adachi, S, Okumura, H, Kouyama, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2002-06-20 | Release date: | 2002-12-18 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin J.MOL.BIOL., 324, 2002
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1B9O
| HUMAN ALPHA-LACTALBUMIN, LOW TEMPERATURE FORM | Descriptor: | CALCIUM ION, PROTEIN (ALPHA-LACTALBUMIN) | Authors: | Harata, K, Abe, Y, Muraki, M. | Deposit date: | 1999-02-14 | Release date: | 1999-03-31 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Crystallographic evaluation of internal motion of human alpha-lactalbumin refined by full-matrix least-squares method. J.Mol.Biol., 287, 1999
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1COP
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1JSF
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1COO
| THE COOH-TERMINAL DOMAIN OF RNA POLYMERASE ALPHA SUBUNIT | Descriptor: | RNA POLYMERASE ALPHA SUBUNIT | Authors: | Jeon, Y.H, Negishi, T, Shirakawa, M, Yamazaki, T, Fujita, N, Ishihama, A, Kyogoku, Y. | Deposit date: | 1995-10-09 | Release date: | 1996-03-08 | Last modified: | 2024-04-10 | Method: | SOLUTION NMR | Cite: | Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science, 270, 1995
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1IQB
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1JSE
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1EHD
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1WLF
| Structure of the N-terminal domain of PEX1 AAA-ATPase: Characterization of a putative adaptor-binding domain | Descriptor: | Peroxisome biogenesis factor 1, SULFATE ION | Authors: | Shiozawa, K, Maita, N, Tomii, K, Seto, A, Goda, N, Tochio, H, Akiyama, Y, Shimizu, T, Shirakawa, M, Hiroaki, H. | Deposit date: | 2004-06-25 | Release date: | 2004-09-07 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Structure of the N-terminal Domain of PEX1 AAA-ATPase: CHARACTERIZATION OF A PUTATIVE ADAPTOR-BINDING DOMAIN J.Biol.Chem., 279, 2004
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1X0S
| Crystal structure of the 13-cis isomer of bacteriorhodopsin | Descriptor: | 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE, 2,3-DI-PHYTANYL-GLYCEROL, Bacteriorhodopsin, ... | Authors: | Nishikawa, T, Murakami, M, Kouyama, T. | Deposit date: | 2005-03-28 | Release date: | 2005-08-30 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state. J.Mol.Biol., 352, 2005
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1WYW
| Crystal Structure of SUMO1-conjugated thymine DNA glycosylase | Descriptor: | CHLORIDE ION, G/T mismatch-specific thymine DNA glycosylase, MAGNESIUM ION, ... | Authors: | Baba, D, Maita, N, Jee, J.G, Uchimura, Y, Saitoh, H, Sugasawa, K, Hanaoka, F, Tochio, H, Hiroaki, H, Shirakawa, M. | Deposit date: | 2005-02-17 | Release date: | 2005-06-21 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature, 435, 2005
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1WR1
| The complex structure of Dsk2p UBA with ubiquitin | Descriptor: | Ubiquitin, Ubiquitin-like protein DSK2 | Authors: | Ohno, A, Jee, J.G, Fujiwara, K, Tenno, T, Goda, N, Tochio, H, Hiroaki, H, kobayashi, H, Shirakawa, M. | Deposit date: | 2004-10-08 | Release date: | 2005-04-19 | Last modified: | 2023-09-27 | Method: | SOLUTION NMR | Cite: | Structure of the UBA domain of Dsk2p in complex with ubiquitin molecular determinants for ubiquitin recognition. Structure, 13, 2005
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