8W2O
 
 | | Yeast U1 snRNP with humanized U1C Zinc-Finger domain | | Descriptor: | 56 kDa U1 small nuclear ribonucleoprotein component, ACT1 pre-mRNA, Pre-mRNA-processing factor 39, ... | | Authors: | Shi, S.S, Kuang, Z.L, Zhao, R. | | Deposit date: | 2024-02-20 | | Release date: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.49 Å) | | Cite: | Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast.
Rna, 2024
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1WX6
 | | Solution structure of the SH3 domain of the human cytoplasmic protein NCK2 | | Descriptor: | Cytoplasmic protein NCK2 | | Authors: | Ohnishi, S, Kigawa, T, Tomizawa, T, Koshiba, S, Inoue, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-01-20 | | Release date: | 2005-07-20 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the SH3 domain of the human cytoplasmic protein NCK2
To be Published
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8J3S
 | | Complex structure of human cytomegalovirus protease and a macrocyclic peptide ligand | | Descriptor: | Assemblin, PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY | | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | | Deposit date: | 2023-04-18 | | Release date: | 2023-11-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.09 Å) | | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
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8J3T
 | | Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand | | Descriptor: | (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin | | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | | Deposit date: | 2023-04-18 | | Release date: | 2023-11-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
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1J3M
 | | Crystal structure of the conserved hypothetical protein TT1751 from Thermus thermophilus HB8 | | Descriptor: | SULFITE ION, the conserved hypothetical protein TT1751 | | Authors: | Kishishita, S, Terada, T, Shirouzu, M, Kuramitsu, S, Park, S.-Y, Tame, R.H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-02-05 | | Release date: | 2004-05-18 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8
Proteins, 57, 2004
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2RQP
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3VJN
 | | Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with AMPPNP. | | Descriptor: | Epidermal growth factor receptor, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER | | Authors: | Yoshikawa, S, Kukimoto-Niino, M, Shirouzu, M, Semba, K, Yamamoto, T, Yokoyama, S. | | Deposit date: | 2011-10-27 | | Release date: | 2012-03-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor.
Oncogene, 32, 2013
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4X0A
 | | Structure of tRNA-processing enzyme complex 6 | | Descriptor: | Poly A polymerase, RNA (73-MER) | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2014-11-21 | | Release date: | 2015-04-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.505 Å) | | Cite: | Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Structure, 23, 2015
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1IQX
 | | CRYSTAL STRUCTURE OF COBALT-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS | | Descriptor: | CO(II)-SUBSTITUTED AMINE OXIDASE, COBALT (II) ION | | Authors: | Kishishita, S, Okajima, T, Mure, M, Kim, M, Yamaguchi, H, Hirota, S, Suzuki, S, Kuroda, S, Tanizawa, K. | | Deposit date: | 2001-08-27 | | Release date: | 2003-02-04 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Role of Copper Ion in Bacterial Copper Amine Oxidase: Spectroscopic and Crystallographic Studies of Metal-Substituted Enzymes
J.AM.CHEM.SOC., 125, 2003
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1IQY
 | | CRYSTAL STRUCTURE OF NICKEL-SUBSTITUTED AMINE OXIDASE FROM ARTHROBACTER GLOBIFORMIS | | Descriptor: | AMINE OXIDASE, NICKEL (II) ION | | Authors: | Kishishita, S, Okajima, T, Mure, M, Kim, M, Yamaguchi, H, Hirota, S, Kuroda, S, Tanizawa, K. | | Deposit date: | 2001-08-28 | | Release date: | 2003-02-04 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Role of Copper Ion in Bacterial Copper Amine Oxidase: Spectroscopic and Crystallographic Studies of Metal-Substituted Enzymes
J.AM.CHEM.SOC., 125, 2003
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5IY5
 | | Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shimada, S, Baba, J, Aoe, S, Shimada, A, Yamashita, E, Tsukihara, T. | | Deposit date: | 2016-03-24 | | Release date: | 2017-01-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode
EMBO J., 36, 2017
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2QZK
 | | Crystal structure of human Beta Secretase complexed with I21 | | Descriptor: | 2-[(5R)-5-amino-5-methyl-4,16-dioxo-14-phenyl-3-oxa-15-azatricyclo[15.3.1.1~7,11~]docosa-1(21),7(22),8,10,12,14,17,19-octaen-19-yl]benzonitrile, Beta-secretase 1 | | Authors: | Munshi, S. | | Deposit date: | 2007-08-16 | | Release date: | 2008-04-29 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Strategies toward improving the brain penetration of macrocyclic tertiary carbinamine BACE-1 inhibitors.
Bioorg.Med.Chem.Lett., 17, 2007
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5WU1
 | | Crystal structure of apo human Tut1, form I | | Descriptor: | CHLORIDE ION, Speckle targeted PIP5K1A-regulated poly(A) polymerase | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2016-12-16 | | Release date: | 2017-05-31 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structures of U6 snRNA-specific terminal uridylyltransferase
Nat Commun, 8, 2017
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5WU6
 | | Crystal structure of apo human Tut1, form IV | | Descriptor: | MAGNESIUM ION, Speckle targeted PIP5K1A-regulated poly(A) polymerase | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2016-12-16 | | Release date: | 2017-05-31 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.209 Å) | | Cite: | Crystal structures of U6 snRNA-specific terminal uridylyltransferase
Nat Commun, 8, 2017
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3VX4
 | | Crystal Structure of the Nucleotide-Binding Domain of S. mutans ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Putative ABC transporter, ... | | Authors: | Ishii, S, Yano, T, Okamoto, A, Murakawa, T, Hayashi, H. | | Deposit date: | 2012-09-11 | | Release date: | 2013-04-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.69 Å) | | Cite: | Boundary of the Nucleotide-Binding Domain of Streptococcus ComA Based on Functional and Structural Analysis
Biochemistry, 52, 2013
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4WBY
 | | tRNA-processing enzyme (apo form I) | | Descriptor: | GLYCEROL, Poly A polymerase, SULFATE ION | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2014-09-04 | | Release date: | 2015-04-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Structure, 23, 2015
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4WC5
 | | Structure of tRNA-processing enzyme complex 3 | | Descriptor: | CYTIDINE-5'-TRIPHOSPHATE, Poly A polymerase, RNA (74-MER) | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2014-09-04 | | Release date: | 2015-04-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.41 Å) | | Cite: | Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Structure, 23, 2015
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4WC4
 | | tRNA-processing enzyme complex 2 | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Poly A polymerase, RNA (74-MER) | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2014-09-04 | | Release date: | 2015-04-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (3.501 Å) | | Cite: | Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Structure, 23, 2015
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1INZ
 | | SOLUTION STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN OF HUMAN EPSIN | | Descriptor: | EPS15-INTERACTING PROTEIN(EPSIN) | | Authors: | Koshiba, S, Kigawa, T, Kikuchi, A, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2000-12-05 | | Release date: | 2001-05-09 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the epsin N-terminal homology (ENTH) domain of human epsin
J.STRUCT.FUNCT.GENOM., 2, 2001
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7XLP
 | | MEK1 bound to DS03090629 | | Descriptor: | (1~{R},3~{S})-3-[[6-[2-chloranyl-4-(4-methylpyrimidin-2-yl)oxy-phenyl]-3-methyl-1~{H}-indazol-4-yl]oxy]cyclohexan-1-amine, CALCIUM ION, DIMETHYL SULFOXIDE, ... | | Authors: | Kishikawa, S, Takano, K, Ubukata, O, Hanzawa, H. | | Deposit date: | 2022-04-22 | | Release date: | 2023-03-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Discovery of a Novel ATP-Competitive MEK Inhibitor DS03090629 that Overcomes Resistance Conferred by BRAF Overexpression in BRAF-Mutated Melanoma.
Mol.Cancer Ther., 22, 2023
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7XNC
 | | MEK1 bound to DS94070624 | | Descriptor: | CALCIUM ION, DIMETHYL SULFOXIDE, Dual specificity mitogen-activated protein kinase kinase 1, ... | | Authors: | Kishikawa, S, Takano, K, Ubukata, O, Hanzawa, H. | | Deposit date: | 2022-04-28 | | Release date: | 2023-03-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Discovery of a Novel ATP-Competitive MEK Inhibitor DS03090629 that Overcomes Resistance Conferred by BRAF Overexpression in BRAF-Mutated Melanoma.
Mol.Cancer Ther., 22, 2023
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1IQ3
 | | SOLUTION STRUCTURE OF THE EPS15 HOMOLOGY DOMAIN OF A HUMAN POB1 | | Descriptor: | CALCIUM ION, RALBP1-INTERACTING PROTEIN (PARTNER OF RALBP1) | | Authors: | Koshiba, S, Kigawa, T, Iwahara, J, Kikuchi, A, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-06-06 | | Release date: | 2001-06-27 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the Eps15 homology domain of a human POB1 (partner of RalBP1).
FEBS Lett., 442, 1999
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8JT1
 | | COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 6-mer peptide, ... | | Authors: | Ueshima, S, Yaskawa, K, Takita, T, Mikami, B. | | Deposit date: | 2023-06-21 | | Release date: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses.
Febs Lett., 597, 2023
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7YTB
 | | Crystal structure of Kin4B8 | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Kin4B8, RETINAL | | Authors: | Murakoshi, S, Chazan, A, Shihoya, W, Beja, O, Nureki, O. | | Deposit date: | 2022-08-14 | | Release date: | 2023-03-15 | | Last modified: | 2023-03-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.
Nature, 615, 2023
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4WC6
 | | Structure of tRNA-processing enzyme complex 4 | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Poly A polymerase, RNA (75-mer) | | Authors: | Yamashita, S, Tomita, K. | | Deposit date: | 2014-09-04 | | Release date: | 2015-04-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.41 Å) | | Cite: | Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.
Structure, 23, 2015
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