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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1B22
 | | RAD51 (N-TERMINAL DOMAIN) | | Descriptor: | DNA REPAIR PROTEIN RAD51 | | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-12-04 | | Release date: | 1999-12-03 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
J.Mol.Biol., 290, 1999
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1P7D
 | | Crystal structure of the Lambda Integrase (residues 75-356) bound to DNA | | Descriptor: | 26-MER, 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3', Integrase | | Authors: | Aihara, H, Kwon, H.J, Nunes-Duby, S.E, Landy, A, Ellenberger, T. | | Deposit date: | 2003-05-01 | | Release date: | 2003-08-12 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase
Mol.Cell, 12, 2003
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2V6E
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6DFY
 | | Remodeled crystal structure of DNA-bound DUX4-HD2 | | Descriptor: | DNA (5'-D(*AP*AP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*GP*T)-3'), DNA (5'-D(*TP*TP*CP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*A)-3'), Double homeobox protein 4 | | Authors: | Aihara, H, Shi, K. | | Deposit date: | 2018-05-15 | | Release date: | 2018-09-05 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.623 Å) | | Cite: | Comment on structural basis of DUX4/IGH-driven transactivation.
Leukemia, 32, 2018
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7R9C
 | | Cocrystal of BRD4(D1) with N,N-dimethyl-2-[(3R)-3-(5-{2-[2-methyl-5-(propan-2-yl)phenoxy]pyrimidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-1-yl)pyrrolidin-1-yl]ethan-1-amine | | Descriptor: | 1,2-ETHANEDIOL, Bromodomain-containing protein 4, CHLORIDE ION, ... | | Authors: | Cui, H, Shi, K, Aihara, H, Pomerantz, W.C.K. | | Deposit date: | 2021-06-29 | | Release date: | 2022-01-19 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes.
J.Med.Chem., 65, 2022
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6U82
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5EJK
 | | Crystal structure of the Rous sarcoma virus intasome | | Descriptor: | DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)-3'), DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*T)-3'), DNA (5'-D(*CP*TP*TP*CP*TP*CP*TP*C)-3'), ... | | Authors: | Yin, Z, Shi, K, Banerjee, S, Aihara, H. | | Deposit date: | 2015-11-02 | | Release date: | 2016-02-17 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (3.8 Å) | | Cite: | Crystal structure of the Rous sarcoma virus intasome.
Nature, 530, 2016
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7UU0
 | | Crystal structure of the BRD2-BD2 in complex with a ligand | | Descriptor: | 1,2-ETHANEDIOL, Isoform 3 of Bromodomain-containing protein 2, methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate | | Authors: | Kalra, P, Shi, K, Aihara, H, Pomerantz, W.C.K. | | Deposit date: | 2022-04-28 | | Release date: | 2023-05-03 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Crystal structure of the BRD2-BD2 in complex with a ligand
To Be Published
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4NQ3
 | | Crystal structure of cyanuic acid hydrolase from A. caulinodans | | Descriptor: | BARBITURIC ACID, Cyanuric acid amidohydrolase, MAGNESIUM ION, ... | | Authors: | Cho, S, Shi, K, Aihara, H. | | Deposit date: | 2013-11-23 | | Release date: | 2014-09-10 | | Method: | X-RAY DIFFRACTION (2.702 Å) | | Cite: | Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.
Plos One, 9, 2014
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8SPI
 | | Crystal structure of chimeric omicron RBD (strain XBB.1.5) complexed with human ACE2 | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Zhang, W, Shi, K, Aihara, H, Li, F. | | Deposit date: | 2023-05-03 | | Release date: | 2023-08-02 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (3.06 Å) | | Cite: | Structural evolution of SARS-CoV-2 omicron in human receptor recognition.
J.Virol., 97, 2023
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8SPH
 | | Crystal structure of chimeric omicron RBD (strain XBB.1) complexed with human ACE2 | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Zhang, W, Shi, K, Aihara, H, Li, F. | | Deposit date: | 2023-05-03 | | Release date: | 2023-08-02 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.71 Å) | | Cite: | Structural evolution of SARS-CoV-2 omicron in human receptor recognition.
J.Virol., 97, 2023
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8SBM
 | | Crystal structure of the wild-type Catalytic ATP-binding domain of Mtb DosS | | Descriptor: | 1,2-ETHANEDIOL, GAF domain-containing protein, SODIUM ION, ... | | Authors: | Larson, G, Shi, K, Aihara, H, Bhagi-Damodaran, A. | | Deposit date: | 2023-04-03 | | Release date: | 2023-11-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.47 Å) | | Cite: | Understanding ATP Binding to DosS Catalytic Domain with a Short ATP-Lid.
Biochemistry, 62, 2023
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6DT1
 | | Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate | | Descriptor: | 2,3-DIHYDROXY-1,4-DITHIOBUTANE, ADENOSINE MONOPHOSPHATE, CHLORIDE ION, ... | | Authors: | Shi, K, Aihara, H. | | Deposit date: | 2018-06-14 | | Release date: | 2018-09-19 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
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6E8C
 | | Crystal structure of the double homeodomain of DUX4 in complex with DNA | | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3'), Double homeobox protein 4 | | Authors: | Lee, J.K, Bosnakovski, D, Toso, E.A, Dinh, T, Banerjee, S, Bohl, T.E, Shi, K, Kurahashi, K, Kyba, M, Aihara, H. | | Deposit date: | 2018-07-27 | | Release date: | 2018-12-26 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.12 Å) | | Cite: | Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA.
Cell Rep, 25, 2018
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6XC1
 | | Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form | | Descriptor: | 1,2-ETHANEDIOL, ISOPROPYL ALCOHOL, Lysozyme, ... | | Authors: | Shi, K, Oakland, J.T, Kurniawan, F, Moeller, N.H, Aihara, H. | | Deposit date: | 2020-06-07 | | Release date: | 2020-12-02 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structural basis of superinfection exclusion by bacteriophage T4 Spackle.
Commun Biol, 3, 2020
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6X6O
 | | Crystal structure of T4 protein Spackle as determined by native SAD phasing | | Descriptor: | CHLORIDE ION, Protein spackle | | Authors: | Shi, K, Kurniawan, F, Banerjee, S, Moeller, N.H, Aihara, H. | | Deposit date: | 2020-05-28 | | Release date: | 2020-09-16 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing.
Acta Crystallogr D Struct Biol, 76, 2020
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6XC0
 | | Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, ... | | Authors: | Shi, K, Oakland, J.T, Kurniawan, F, Moeller, N.H, Aihara, H. | | Deposit date: | 2020-06-07 | | Release date: | 2020-12-02 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Structural basis of superinfection exclusion by bacteriophage T4 Spackle.
Commun Biol, 3, 2020
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5HX5
 | | APOBEC3F Catalytic Domain Crystal Structure | | Descriptor: | DNA dC->dU-editing enzyme APOBEC-3F, ZINC ION | | Authors: | Shaban, N.M, Shi, K, Aihara, H, Harris, R.S. | | Deposit date: | 2016-01-29 | | Release date: | 2016-05-18 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.33 Å) | | Cite: | 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.
J.Mol.Biol., 428, 2016
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5HX4
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5IRS
 | | crystal structure of the proteasomal Rpn13 PRU-domain | | Descriptor: | 2,3-DIHYDROXY-1,4-DITHIOBUTANE, Proteasomal ubiquitin receptor ADRM1 | | Authors: | Chen, X, Shi, K, Walters, K, Aihara, H. | | Deposit date: | 2016-03-14 | | Release date: | 2016-07-20 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.796 Å) | | Cite: | Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.
Structure, 24, 2016
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6O44
 | | Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, Nattokinase, ... | | Authors: | Tang, H, Shi, K, Aihara, H. | | Deposit date: | 2019-02-28 | | Release date: | 2019-04-10 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis.
Biochem. Biophys. Res. Commun., 512, 2019
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6PAK
 | | Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, Subtilisin E | | Authors: | Tang, H, Shi, K, Aihara, H. | | Deposit date: | 2019-06-11 | | Release date: | 2019-10-23 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy.
J.Biol.Chem., 294, 2019
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7MLS
 | | X-ray crystal structure of human BRD4(D1) in complex with 2-(2,5-dibromophenoxy)-6-[4-methyl-1-(piperidin-4-yl)-1H-1,2,3-triazol-5-yl]pyridine (compound 23) | | Descriptor: | 1,2-ETHANEDIOL, 2-(2,5-dibromophenoxy)-6-[4-methyl-1-(piperidin-4-yl)-1H-1,2,3-triazol-5-yl]pyridine, Bromodomain-containing protein 4, ... | | Authors: | Cui, H, Johnson, J.A, Zahid, H, Buchholz, C.R, Shi, K, Aihara, H, Pomerantz, W.C.K. | | Deposit date: | 2021-04-28 | | Release date: | 2021-07-28 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.26 Å) | | Cite: | 4-Methyl-1,2,3-Triazoles as N -Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity.
J.Med.Chem., 64, 2021
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5SXG
 | | Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B | | Descriptor: | 1,3-PROPANDIOL, DNA dC->dU-editing enzyme APOBEC-3B, IMIDAZOLE, ... | | Authors: | Shi, K, Kurahashi, K, Aihara, H. | | Deposit date: | 2016-08-09 | | Release date: | 2017-12-27 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Sci Rep, 7, 2017
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