8J3R
 
 | | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-18 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (2.95 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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5Y5N
 | | Crystal structure of human Sirtuin 2 in complex with a selective inhibitor | | Descriptor: | 2-[[3-(2-phenylethoxy)phenyl]amino]benzamide, NAD-dependent protein deacetylase sirtuin-2, ZINC ION | | Authors: | Mellini, P, Itoh, Y, Tsumoto, H, Li, Y, Suzuki, M, Tokuda, N, Kakizawa, T, Miura, Y, Takeuchi, J, Lahtela-Kakkonen, M, Suzuki, T. | | Deposit date: | 2017-08-09 | | Release date: | 2017-09-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Potent mechanism-based sirtuin-2-selective inhibition by anin situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Chem Sci, 8, 2017
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8HIO
 | | Cryo-EM structure of the Cas12m2-crRNA binary complex | | Descriptor: | Cas12m2, MAGNESIUM ION, RNA (56-MER), ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-21 | | Release date: | 2023-04-12 | | Last modified: | 2023-08-30 | | Method: | ELECTRON MICROSCOPY (3.73 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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8HHM
 | | Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state | | Descriptor: | Cas12m2, DNA (36-MER), MAGNESIUM ION, ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-16 | | Release date: | 2023-04-12 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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8HHL
 | | Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex | | Descriptor: | Cas12m2, MAGNESIUM ION, NTS (36-MER), ... | | Authors: | Omura, N.S, Nakagawa, R, Wu, Y.W, Sudfeld, C, Warren, V.R, Hirano, H, Kusakizako, T, Kise, Y, Lebbink, H.G.J, Itoh, Y, Oost, V.D.J, Nureki, O. | | Deposit date: | 2022-11-16 | | Release date: | 2023-04-12 | | Last modified: | 2023-08-30 | | Method: | ELECTRON MICROSCOPY (2.87 Å) | | Cite: | Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Nat.Struct.Mol.Biol., 30, 2023
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3WVQ
 | | Structure of ATP grasp protein | | Descriptor: | GLYCEROL, PGM1, SULFATE ION | | Authors: | Matsui, T, Noike, M, Ooya, K, Sasaki, I, Hamano, Y, Maruyama, C, Ishikawa, J, Satoh, Y, Ito, H, Dairi, T, Morita, H. | | Deposit date: | 2014-06-04 | | Release date: | 2014-11-19 | | Last modified: | 2014-12-31 | | Method: | X-RAY DIFFRACTION (1.955 Å) | | Cite: | A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin.
Nat.Chem.Biol., 11, 2015
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3WVR
 | | Structure of ATP grasp protein with AMP | | Descriptor: | ADENOSINE MONOPHOSPHATE, GLYCEROL, PGM1, ... | | Authors: | Matsui, T, Noike, M, Ooya, K, Sasaki, I, Hamano, Y, Maruyama, C, Ishikawa, J, Satoh, Y, Ito, H, Dairi, T, Morita, H. | | Deposit date: | 2014-06-04 | | Release date: | 2014-11-19 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.175 Å) | | Cite: | A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin.
Nat.Chem.Biol., 11, 2015
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6IKO
 | | Crystal structure of mouse GAS7cb | | Descriptor: | Growth arrest-specific protein 7 | | Authors: | Hanawa-Suetsugu, K, Itoh, Y, Kohda, D, Shimada, A, Suetsugu, S. | | Deposit date: | 2018-10-16 | | Release date: | 2019-10-16 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.756 Å) | | Cite: | Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7.
Nat Commun, 10, 2019
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6IKN
 | | Crystal structure of the GAS7 F-BAR domain | | Descriptor: | Growth arrest-specific protein 7 | | Authors: | Hanawa-Suetsugu, K, Itoh, Y, Kohda, D, Shimada, A, Suetsugu, S. | | Deposit date: | 2018-10-16 | | Release date: | 2019-10-16 | | Last modified: | 2019-10-30 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7.
Nat Commun, 10, 2019
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3C7X
 | | Hemopexin-like domain of matrix metalloproteinase 14 | | Descriptor: | CHLORIDE ION, Matrix metalloproteinase-14, SODIUM ION | | Authors: | Tochowicz, A, Itoh, Y, Maskos, K, Bode, W, Goettig, P. | | Deposit date: | 2008-02-08 | | Release date: | 2009-02-10 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | The dimer interface of the membrane type 1 matrix metalloproteinase hemopexin domain: crystal structure and biological functions
J.Biol.Chem., 286, 2011
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3WO9
 | | Crystal structure of the lamprey variable lymphocyte receptor C | | Descriptor: | Variable lymphocyte receptor C | | Authors: | Kanda, R, Sutoh, Y, Kasamatsu, J, Maenaka, K, Kasahara, M, Ose, T. | | Deposit date: | 2013-12-20 | | Release date: | 2014-03-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of the lamprey variable lymphocyte receptor C reveals an unusual feature in its N-terminal capping module.
Plos One, 9, 2014
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5IBV
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2ZOD
 | | Crystal structure of selenophosphate synthetase from Aquifex aeolicus | | Descriptor: | SULFATE ION, Selenide, water dikinase | | Authors: | Sekine, S.I, Matsumoto, E, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-05-09 | | Release date: | 2008-05-27 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs.
J.Mol.Biol., 385, 2009
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5I61
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5I62
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3IWR
 | | Crystal structure of class I chitinase from Oryza sativa L. japonica | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Chitinase | | Authors: | Kezuka, Y, Watanabe, T, Nonaka, T. | | Deposit date: | 2009-09-03 | | Release date: | 2010-04-21 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.57 Å) | | Cite: | Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
Proteins, 78, 2010
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1WVU
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1WVV
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2DBT
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3O95
 | | Crystal Structure of Human DPP4 Bound to TAK-100 | | 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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Yano, J.K, Aertgeerts, K. | | Deposit date: | 2010-08-03 | | Release date: | 2011-01-26 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor.
J.Med.Chem., 53, 2011
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3O9V
 | | Crystal Structure of Human DPP4 Bound to TAK-986 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 5-(aminomethyl)-2-methyl-4-(4-methylphenyl)-6-(2-methylpropyl)pyridine-3-carboxic acid, ... | | Authors: | Yano, J.K, Aertgeerts, K. | | Deposit date: | 2010-08-04 | | Release date: | 2011-02-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor.
J.Med.Chem., 53, 2011
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6JUW
 | | BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 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, A, Muramoto, K, Shinzawa-Itoh, K, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2019-04-15 | | Release date: | 2020-03-25 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | X-ray structures of catalytic intermediates of cytochromecoxidase provide insights into its O2activation and unidirectional proton-pump mechanisms.
J.Biol.Chem., 295, 2020
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5AVE
 | | The ligand binding domain of Mlp37 with serine | | Descriptor: | Methyl-accepting chemotaxis (MCP) signaling domain protein, SERINE | | Authors: | Takahashi, Y, Sumita, K, Uchida, Y, Nishiyama, S, Kawagishi, I, Imada, K. | | Deposit date: | 2015-06-15 | | Release date: | 2016-03-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants
Sci Rep, 6, 2016
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5AVF
 | | The ligand binding domain of Mlp37 with taurine | | Descriptor: | 2-AMINOETHANESULFONIC ACID, Methyl-accepting chemotaxis (MCP) signaling domain protein | | Authors: | Takahashi, Y, Sumita, K, Uchida, Y, Nishiyama, S, Kawagishi, I, Imada, K. | | Deposit date: | 2015-06-15 | | Release date: | 2016-06-01 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Identification of a Vibrio cholerae chemoreceptor that senses taurine and amino acids as attractants
Sci Rep, 6, 2016
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3A8E
 | | The structure of AxCesD octamer complexed with cellopentaose | | Descriptor: | Cellulose synthase operon protein D, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose | | Authors: | Hu, S.Q, Tajima, K, Zhou, Y, Yao, M, Tanaka, I. | | Deposit date: | 2009-10-05 | | Release date: | 2010-09-22 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of bacterial cellulose synthase subunit D octamer with four inner passageways
Proc.Natl.Acad.Sci.USA, 107, 2010
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