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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8VQR
 | | Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2 | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Hsueh, F.-C, Shi, K, Aihara, H, Li, F. | | Deposit date: | 2024-01-19 | | Release date: | 2024-05-01 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2.565 Å) | | Cite: | Structural basis for raccoon dog receptor recognition by SARS-CoV-2
To Be Published
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8FR5
 | | Crystal structure of the Human Smacovirus 1 Rep domain | | Descriptor: | MANGANESE (II) ION, Rep, SODIUM ION | | Authors: | Limon, L.K, Shi, K, Dao, A, Rugloski, J, Tompkins, K.J, Aihara, H, Gordon, W.R, Evans IIII, R.L. | | Deposit date: | 2023-01-06 | | Release date: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | The crystal structure of the human smacovirus 1 Rep domain.
Acta Crystallogr.,Sect.F, 79, 2023
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3I41
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3I48
 | | Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound magnesium ions | | Descriptor: | Beta-hemolysin, MAGNESIUM ION, PHOSPHATE ION | | Authors: | Huseby, M, Shi, K, Kruse, A.C, Ohlendorf, D.H. | | Deposit date: | 2009-07-01 | | Release date: | 2010-07-14 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence
to be published, 2009
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3I5V
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3I46
 | | Crystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound calcium ions | | Descriptor: | Beta-hemolysin, CALCIUM ION, CHLORIDE ION | | Authors: | Huseby, M, Shi, K, Kruse, A.C, Ohlendorf, D.H. | | Deposit date: | 2009-07-01 | | Release date: | 2010-07-14 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence
To be Published
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5E96
 | | Crystal structure of aminoglycoside 6'-acetyltransferase type Ii | | Descriptor: | 1,2-ETHANEDIOL, Aminoglycoside 6'-acetyltransferase, PHOSPHATE ION | | Authors: | Berghuis, A.M, Burk, D.L, Baettig, O.M, Shi, K. | | Deposit date: | 2015-10-14 | | Release date: | 2016-07-06 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Comprehensive characterization of ligand-induced plasticity changes in a dimeric enzyme.
Febs J., 283, 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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4EP4
 | | Thermus thermophilus RuvC structure | | Descriptor: | Crossover junction endodeoxyribonuclease RuvC, GLYCEROL, MAGNESIUM ION | | Authors: | Chen, L, Shi, K, Yin, Z.Q, Aihara, H. | | Deposit date: | 2012-04-17 | | Release date: | 2012-11-14 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.28 Å) | | Cite: | Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.
Nucleic Acids Res., 41, 2013
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4EP5
 | | Thermus thermophilus RuvC structure | | Descriptor: | Crossover junction endodeoxyribonuclease RuvC, GLYCEROL, SULFATE ION | | Authors: | Chen, L, Shi, K, Yin, Z.Q, Aihara, H. | | Deposit date: | 2012-04-17 | | Release date: | 2012-11-14 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.
Nucleic Acids Res., 41, 2013
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7JN3
 | | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048 | | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | | Deposit date: | 2020-08-03 | | Release date: | 2021-03-17 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.21 Å) | | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome.
Commun Biol, 4, 2021
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7KUI
 | | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. CIC region of a cluster identified by 3-dimensional variability analysis in cryoSPARC. | | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | | Deposit date: | 2020-11-25 | | Release date: | 2021-03-17 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome.
Commun Biol, 4, 2021
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7KU7
 | | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. Cluster identified by 3-dimensional variability analysis in cryoSPARC. | | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | | Deposit date: | 2020-11-24 | | Release date: | 2021-03-17 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome.
Commun Biol, 4, 2021
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7MC6
 | | Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, MAGNESIUM ION, ... | | Authors: | Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H. | | Deposit date: | 2021-04-01 | | Release date: | 2021-05-05 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7MC5
 | | Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, L(+)-TARTARIC ACID, ... | | Authors: | Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H. | | Deposit date: | 2021-04-01 | | Release date: | 2021-05-05 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.64 Å) | | Cite: | Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
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3K55
 | | Structure of beta hairpin deletion mutant of beta toxin from Staphylococcus aureus | | Descriptor: | Beta-hemolysin, CHLORIDE ION, SODIUM ION | | Authors: | Kruse, A.C, Huseby, M, Shi, K, Digre, J, Ohlendorf, D.H, Earhart, C.A. | | Deposit date: | 2009-10-06 | | Release date: | 2011-01-26 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (3.35 Å) | | Cite: | Structure of a mutant beta toxin from Staphylococcus aureus reveals domain swapping and conformational flexibility
Acta Crystallogr.,Sect.F, 67, 2011
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3LMX
 | | Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis | | Descriptor: | 3,4-DIHYDROXYBENZOIC ACID, BETA-MERCAPTOETHANOL, CHLORIDE ION, ... | | Authors: | Purpero, V.M, Lipscomb, J.D, Shi, K. | | Deposit date: | 2010-02-01 | | Release date: | 2011-02-16 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis
To be Published
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7KIJ
 | | Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site | | Descriptor: | ATP-dependent helicase Rep, DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3'), GLYCEROL, ... | | Authors: | Tompkins, K.J, Gordon, W.R, Shi, K. | | Deposit date: | 2020-10-23 | | Release date: | 2021-11-17 | | Last modified: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.
Mbio, 14, 2023
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7M8R
 | | Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans | | Descriptor: | 1,1,1-tris(fluoranyl)propan-2-one, 1,2-ETHANEDIOL, BENZOIC ACID, ... | | Authors: | Johns, J.C, Banerjee, R, Shi, K, Semonis, M.M, Aihara, H, Pomerantz, W.C.K, Lipscomb, J.D. | | Deposit date: | 2021-03-30 | | Release date: | 2021-07-28 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.22 Å) | | Cite: | Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR.
Biochemistry, 60, 2021
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7M8Q
 | | Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans | | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | | Authors: | Johns, J.C, Banerjee, R, Shi, K, Semonis, M.M, Aihara, H, Pomerantz, W.C.K, Lipscomb, J.D. | | Deposit date: | 2021-03-30 | | Release date: | 2021-07-28 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR.
Biochemistry, 60, 2021
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6B0B
 | | Crystal structure of human APOBEC3H | | Descriptor: | APOBEC3H, MCherry, RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3'), ... | | Authors: | Shaban, N.M, Shi, K, Banerjee, S, Harris, R.S, Aihara, H. | | Deposit date: | 2017-09-14 | | Release date: | 2017-10-25 | | Last modified: | 2019-12-04 | | Method: | X-RAY DIFFRACTION (3.2800622 Å) | | Cite: | The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.
Mol. Cell, 69, 2018
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6BBO
 | | Crystal structure of human APOBEC3H/RNA complex | | Descriptor: | APOBEC3H, GLYCEROL, MCherry fluorescent protein, ... | | Authors: | Shaban, N.M, Shi, K, Banerjee, S, Harris, R.S, Aihara, H. | | Deposit date: | 2017-10-19 | | Release date: | 2018-01-10 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.428 Å) | | Cite: | The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.
Mol. Cell, 69, 2018
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7KM6
 | | APOBEC3B antibody 5G7 Fv-clasp | | Descriptor: | 1,2-ETHANEDIOL, 5G7 human monoclonal FAB heavy chain, 5G7 human monoclonal FAB light chain, ... | | Authors: | Tang, H, Shi, K, Aihara, H. | | Deposit date: | 2020-11-02 | | Release date: | 2021-05-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.67 Å) | | Cite: | Structural Characterization of a Minimal Antibody against Human APOBEC3B.
Viruses, 13, 2021
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7KII
 | | Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+ | | Descriptor: | ATP-dependent helicase Rep, CALCIUM ION, DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3'), ... | | Authors: | Tompkins, K.J, Gordon, W.R, Shi, K. | | Deposit date: | 2020-10-23 | | Release date: | 2021-11-17 | | Last modified: | 2024-06-19 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.
Mbio, 14, 2023
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