3GFI
 
 | | Crystal structure of ST1710 complexed with its promoter DNA | | Descriptor: | 146aa long hypothetical transcriptional regulator, 5'-D(*TP*AP*AP*CP*AP*AP*TP*AP*GP*CP*AP*AP*A)-3', 5'-D(*TP*TP*GP*CP*TP*AP*TP*TP*GP*T)-3' | | Authors: | Kumarevel, T, Tanaka, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-02-26 | | Release date: | 2009-08-25 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
Nucleic Acids Res., 37, 2009
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3GH7
 | | Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GalNAc | | Descriptor: | 2-acetamido-2-deoxy-beta-D-galactopyranose, SULFATE ION, beta-hexosaminidase | | Authors: | Sumida, T, Ishii, R, Yanagisawa, T, Yokoyama, S, Ito, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-03-03 | | Release date: | 2009-07-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids
J.Mol.Biol., 392, 2009
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3GH4
 | | Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 | | Descriptor: | ACETIC ACID, SULFATE ION, beta-hexosaminidase | | Authors: | Sumida, T, Ishii, R, Yanagisawa, T, Yokoyama, S, Ito, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-03-03 | | Release date: | 2009-07-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids
J.Mol.Biol., 392, 2009
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3B13
 | | Crystal structure of the DHR-2 domain of DOCK2 in complex with Rac1 (T17N mutant) | | Descriptor: | Dedicator of cytokinesis protein 2, Ras-related C3 botulinum toxin substrate 1 | | Authors: | Hanawa-Suetsugu, K, Kukimoto-Niino, M, Mishima-Tsumagari, C, Terada, T, Shirouzu, M, Fukui, Y, Yokoyama, S. | | Deposit date: | 2011-06-24 | | Release date: | 2012-03-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.006 Å) | | Cite: | Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.
Proc.Natl.Acad.Sci.USA, 109, 2012
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1IYF
 | | Solution structure of ubiquitin-like domain of human parkin | | Descriptor: | parkin | | Authors: | Sakata, E, Yamaguchi, Y, Kurimoto, E, Kikuchi, J, Yokoyama, S, Kawahara, H, Yokosawa, H, Hattori, N, Mizuno, Y, Tanaka, K, Kato, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-08-13 | | Release date: | 2003-03-25 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
EMBO REP., 4, 2003
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1IVZ
 | | Solution structure of the SEA domain from murine hypothetical protein homologous to human mucin 16 | | Descriptor: | hypothetical protein 1110008I14RIK | | Authors: | Maeda, T, Inoue, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-04-02 | | Release date: | 2002-10-02 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
J.Biol.Chem., 279, 2004
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6LR2
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3VU8
 | | Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue | | Descriptor: | Methionine--tRNA ligase, N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE, ZINC ION | | Authors: | Konno, M, Kato-Murayama, M, Toma-Fukai, S, Uchikawa, E, Nureki, O, Yokoyama, S. | | Deposit date: | 2012-06-22 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases
To be Published
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2ZZM
 | | The complex structure of aTrm5 and tRNALeu | | Descriptor: | MAGNESIUM ION, RNA (84-MER), S-ADENOSYLMETHIONINE, ... | | Authors: | Goto-Ito, S, Ito, T, Yokoyama, S. | | Deposit date: | 2009-02-19 | | Release date: | 2009-09-15 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation
Nat.Struct.Mol.Biol., 16, 2009
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3ABH
 | | Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.0 A) | | Descriptor: | Protein kinase C and casein kinase substrate in neurons protein 2 | | Authors: | Shimada, A, Shirouzu, M, Hanawa-Suetsugu, K, Terada, T, Umehara, T, Suetsugu, S, Yamamoto, M, Yokoyama, S. | | Deposit date: | 2009-12-11 | | Release date: | 2010-04-14 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II
Febs Lett., 584, 2010
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3ACO
 | | Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.7 A) | | Descriptor: | CALCIUM ION, Protein kinase C and casein kinase substrate in neurons protein 2 | | Authors: | Shimada, A, Shirouzu, M, Hanawa-Suetsugu, K, Terada, T, Umehara, T, Suetsugu, S, Yamamoto, M, Yokoyama, S. | | Deposit date: | 2010-01-07 | | Release date: | 2010-04-14 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II
Febs Lett., 584, 2010
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5XJ0
 | | T. thermophilus RNA polymerase holoenzyme bound with gp39 and gp76 | | Descriptor: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | Authors: | Ooi, W.Y, Murayama, Y, Mekler, V, Minakhin, L, Severinov, K, Yokoyama, S, Sekine, S. | | Deposit date: | 2017-04-28 | | Release date: | 2017-12-20 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (4.004 Å) | | Cite: | A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation
Nucleic Acids Res., 46, 2018
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3AOU
 | | Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of the Na+-transporting V-ATPase | | Descriptor: | DICYCLOHEXYLUREA, UNDECYL-MALTOSIDE, V-type sodium ATPase subunit K | | Authors: | Mizutani, K, Yamamoto, M, Yamato, I, Kakinuma, Y, Shirouzu, M, Yokoyama, S, Iwata, S, Murata, T. | | Deposit date: | 2010-10-06 | | Release date: | 2011-08-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.14 Å) | | Cite: | Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase.
Proc.Natl.Acad.Sci.USA, 108, 2011
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3AJE
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3AQE
 | | Crystal structure of the extracellular domain of human RAMP2 | | Descriptor: | Receptor activity-modifying protein 2 | | Authors: | Kusano, S, Kukimoto-Niino, M, Shirouzu, M, Shindo, T, Yokoyama, S. | | Deposit date: | 2010-10-29 | | Release date: | 2011-11-09 | | Last modified: | 2012-07-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding
Protein Sci., 21, 2012
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3AY0
 | | Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine | | Descriptor: | ADENOSINE, Uncharacterized protein MJ0883, ZINC ION | | Authors: | Goto-Ito, S, Ito, T, Hou, Y.M, Yokoyama, S. | | Deposit date: | 2011-04-21 | | Release date: | 2011-08-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.05 Å) | | Cite: | Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.
Rna, 17, 2011
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3AQF
 | | Crystal structure of the human CRLR/RAMP2 extracellular complex | | Descriptor: | Calcitonin gene-related peptide type 1 receptor, Receptor activity-modifying protein 2 | | Authors: | Kusano, S, Kukimono-Niino, M, Shirouzu, M, Shindo, T, Yokoyama, S. | | Deposit date: | 2010-10-29 | | Release date: | 2011-11-02 | | Last modified: | 2012-07-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding
Protein Sci., 21, 2012
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3AXZ
 | | Crystal structure of Haemophilus influenzae TrmD in complex with adenosine | | Descriptor: | ADENOSINE, tRNA (guanine-N(1)-)-methyltransferase | | Authors: | Yoshida, K, Goto-Ito, S, Ito, T, Hou, Y.M, Yokoyama, S. | | Deposit date: | 2011-04-21 | | Release date: | 2011-08-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.
Rna, 17, 2011
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1IV0
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3CM0
 | | Crystal structure of adenylate kinase from Thermus thermophilus HB8 | | Descriptor: | Adenylate kinase | | Authors: | Nakagawa, N, Kondo, N, Masui, R, Matsuda, Z, Iwamoto, I, Yokoyama, S, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-03-20 | | Release date: | 2008-09-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of adenylate kinase from Thermus thermophilus HB8
To be Published
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3CPQ
 | | Crystal Structure of L30e a ribosomal protein from Methanocaldococcus jannaschii DSM2661 (MJ1044) | | Descriptor: | 50S ribosomal protein L30e | | Authors: | Jeyakanthan, J, Sarani, R, Mridula, P, Sekar, K, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-04-01 | | Release date: | 2009-04-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal Structure of L30e a ribosomal protein from Methanocaldococcus jannaschii DSM2661 (MJ1044)
To be Published
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3AFH
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5AV9
 | | human nucleosome core particle | | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | | Deposit date: | 2015-06-12 | | Release date: | 2015-12-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation
Sci Rep, 5, 2015
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5B2J
 | | Human nucleosome containing CpG methylated DNA | | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Fujii, Y, Wakamori, M, Umehara, T, Yokoyama, S. | | Deposit date: | 2016-01-18 | | Release date: | 2016-06-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation.
Febs Open Bio, 6, 2016
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5AV8
 | | human nucleosome core particle | | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | | Deposit date: | 2015-06-12 | | Release date: | 2015-12-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation
Sci Rep, 5, 2015
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