2D7R
 
 | | Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on lectin domain | | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Kubota, T, Shiba, T, Sugioka, S, Kato, R, Wakatsuki, S, Narimatsu, H. | | Deposit date: | 2005-11-25 | | Release date: | 2006-11-07 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10)
J.Mol.Biol., 359, 2006
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2DWX
 | | Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif | | Descriptor: | ADP-ribosylation factor-binding protein GGA1, hinge peptide from ADP-ribosylation factor binding protein GGA1 | | Authors: | Inoue, M, Shiba, T, Yamada, Y, Ihara, K, Kawasaki, M, Kato, R, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2006-08-21 | | Release date: | 2007-04-17 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Traffic, 8, 2007
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2DWY
 | | Crystal Structure Analysis of GGA1-GAE | | Descriptor: | ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1 | | Authors: | Inoue, M, Shiba, T, Yamada, Y, Ihara, K, Kawasaki, M, Kato, R, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2006-08-21 | | Release date: | 2007-04-17 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Traffic, 8, 2007
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1EW1
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2RPD
 | | Mhr1p-bound ssDNA | | Descriptor: | DNA (5'-D(*DTP*DAP*DCP*DG)-3') | | Authors: | Masuda, T, Ito, Y, Shibata, T, Mikawa, T. | | Deposit date: | 2008-05-15 | | Release date: | 2009-05-26 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
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4TWZ
 | | Crystal Structure Analysis of E Coli. RecA Protein | | Descriptor: | MAGNESIUM ION, Protein RecA | | Authors: | Hikima, T, Hiraki, T, Furuse, M, Ikawa, S, Iwasaki, W, Shibata, T, Kamiya, N. | | Deposit date: | 2014-07-02 | | Release date: | 2015-07-08 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair
Nucleic Acids Res., 43, 2015
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4R07
 | | Crystal structure of human TLR8 in complex with ORN06 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate), ... | | Authors: | Tanji, H, Ohto, U, Shibata, T, Taoka, M, Yamauchi, Y, Isobe, T, Miyake, K, Shimizu, T. | | Deposit date: | 2014-07-30 | | Release date: | 2015-01-14 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Toll-like receptor 8 senses degradation products of single-stranded RNA
Nat.Struct.Mol.Biol., 22, 2015
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8JCD
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8JBX
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3GJL
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3', SODIUM ION | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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3GJJ
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, 5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3' | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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3GJK
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3', POTASSIUM ION | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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8JCC
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2RPF
 | | RecO-bound ssDNA | | Descriptor: | DNA (5'-D(*DTP*DAP*DCP*DG)-3') | | Authors: | Masuda, T, Ito, Y, Shibata, T, Mikawa, T. | | Deposit date: | 2008-05-15 | | Release date: | 2009-05-26 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
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2RPH
 | | RecT-bound ssDNA | | Descriptor: | DNA (5'-D(*DTP*DAP*DCP*DG)-3') | | Authors: | Masuda, T, Ito, Y, Shibata, T, Mikawa, T. | | Deposit date: | 2008-05-15 | | Release date: | 2009-05-26 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
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3REC
 | | ESCHERICHIA COLI RECA PROTEIN-BOUND DNA, NMR, 1 STRUCTURE | | Descriptor: | DNA (5'-D(*TP*A)-3') | | Authors: | Nishinaka, T, Ito, Y, Yokoyama, S, Shibata, T. | | Deposit date: | 1997-04-17 | | Release date: | 1997-10-22 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | An extended DNA structure through deoxyribose-base stacking induced by RecA protein.
Proc.Natl.Acad.Sci.USA, 94, 1997
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2RPE
 | | hsRad51-bound ssDNA | | Descriptor: | DNA (5'-D(*DTP*DAP*DCP*DG)-3') | | Authors: | Masuda, T, Ito, Y, Shibata, T, Mikawa, T. | | Deposit date: | 2008-05-15 | | Release date: | 2009-05-26 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | A non-canonical DNA structure enables homologous recombination in various genetic systems
J.Biol.Chem., 284, 2009
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6IQE
 | | Human prohibitin 2 | | Descriptor: | Prohibitin-2 | | Authors: | Hirano, Y, Koshiba, T, Tamada, T. | | Deposit date: | 2018-11-07 | | Release date: | 2019-09-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.701 Å) | | Cite: | Structural Basis of Mitochondrial Scaffolds by Prohibitin Complexes: Insight into a Role of the Coiled-Coil Region.
Iscience, 19, 2019
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1AA3
 | | C-TERMINAL DOMAIN OF THE E. COLI RECA, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | RECA | | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Terada, T, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1997-01-22 | | Release date: | 1997-07-23 | | Last modified: | 2024-04-10 | | Method: | SOLUTION NMR | | Cite: | An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing.
J.Mol.Biol., 274, 1997
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1CKK
 | | CALMODULIN/RAT CA2+/CALMODULIN DEPENDENT PROTEIN KINASE FRAGMENT | | Descriptor: | CALCIUM ION, Calcium/calmodulin-dependent protein kinase kinase 1, Calmodulin-1 | | Authors: | Osawa, M, Tokumitsu, H, Swindells, M.B, Kurihara, H, Orita, M, Shibanuma, T, Furuya, T, Ikura, M. | | Deposit date: | 1998-11-20 | | Release date: | 1999-09-10 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase.
Nat.Struct.Biol., 6, 1999
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1IPA
 | | CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE | | Descriptor: | RNA 2'-O-RIBOSE METHYLTRANSFERASE | | Authors: | Nureki, O, Shirouzu, M, Hashimoto, K, Ishitani, R, Terada, T, Tamakoshi, M, Oshima, T, Chijimatsu, M, Takio, K, Vassylyev, D.G, Shibata, T, Inoue, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-05-02 | | Release date: | 2002-07-10 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | An enzyme with a deep trefoil knot for the active-site architecture.
Acta Crystallogr.,Sect.D, 58, 2002
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1J1H
 | | Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus | | Descriptor: | Small Protein B | | Authors: | Someya, T, Nameki, N, Hosoi, H, Suzuki, S, Hatanaka, H, Fujii, M, Terada, T, Shirouzu, M, Inoue, Y, Shibata, T, Kuramitsu, S, Yokoyama, S, Kawai, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-04 | | Release date: | 2003-02-11 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus
FEBS Lett., 535, 2003
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6IZP
 | | Solution structure of the complex of naphthyridine carbamate dimer and an RNA with UGGAA-UGGAA pentad | | Descriptor: | 3-[3-[(7-methyl-1,8-naphthyridin-2-yl)carbamoyloxy]propylamino]propyl ~{N}-(7-methyl-1,8-naphthyridin-2-yl)carbamate, RNA (29-MER) | | Authors: | Nagano, K, Shibata, T, Nakatani, K, Kawai, G. | | Deposit date: | 2018-12-20 | | Release date: | 2019-12-25 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model
Nat Commun, 12, 2021
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5XL0
 | | met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain | | Descriptor: | Myoglobin, SULFATE ION, fluorinated heme | | Authors: | Kanai, Y, Harada, A, Shibata, T, Nishimura, R, Namiki, K, Watanabe, M, Nakamura, S, Yumoto, F, Senda, T, Suzuki, A, Neya, S, Yamamoto, Y. | | Deposit date: | 2017-05-10 | | Release date: | 2017-08-16 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor
Biochemistry, 56, 2017
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3AUJ
 | | Structure of diol dehydratase complexed with glycerol | | Descriptor: | CALCIUM ION, COBALAMIN, Diol dehydrase alpha subunit, ... | | Authors: | Yamanishi, M, Kinoshita, K, Fukuoka, M, Shibata, T, Tobimatsu, T, Toraya, T. | | Deposit date: | 2011-02-07 | | Release date: | 2012-02-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols
Febs J., 279, 2012
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