8E14
| Cryo-EM structure of Rous sarcoma virus strand transfer complex | Descriptor: | DNA (42-MER), 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*TP*CP*TP*TP*CP*TP*TP*TP*C)-3'), ... | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | Deposit date: | 2022-08-09 | Release date: | 2023-04-26 | Last modified: | 2023-10-18 | Method: | ELECTRON MICROSCOPY (3.36 Å) | Cite: | Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. J.Biol.Chem., 299, 2023
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8E5D
| Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine parked in the major groove | Descriptor: | DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'), Double-stranded DNA deaminase toxin A, MAGNESIUM ION, ... | Authors: | Yin, L.L, Shi, K, Aihara, H. | Deposit date: | 2022-08-21 | Release date: | 2023-05-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.39 Å) | Cite: | Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat.Struct.Mol.Biol., 30, 2023
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8E5E
| Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site | Descriptor: | DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3'), DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'), Double-stranded DNA deaminase toxin A, ... | Authors: | Yin, L.L, Shi, K, Aihara, H. | Deposit date: | 2022-08-21 | Release date: | 2023-05-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.62 Å) | Cite: | Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA. Nat.Struct.Mol.Biol., 30, 2023
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8EJO
| Crystal structure of the homeodomain of Platypus sDUX in complex with DNA | Descriptor: | 1,2-ETHANEDIOL, 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'), ... | Authors: | Yin, L.L, Shi, K, Aihara, H. | Deposit date: | 2022-09-18 | Release date: | 2023-09-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.67 Å) | Cite: | Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein. Iscience, 26, 2023
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8EJP
| Crystal structure of the homeodomain of Platypus sDUX in complex with DNA containing 5-Bromouracil | Descriptor: | 1,2-ETHANEDIOL, 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'), ... | Authors: | Yin, L.L, Shi, K, Aihara, H. | Deposit date: | 2022-09-18 | Release date: | 2023-09-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.174 Å) | Cite: | Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein. Iscience, 26, 2023
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8EUO
| Hydroxynitrile Lyase from Hevea brasiliensis with Seven Mutations | Descriptor: | (S)-hydroxynitrile lyase | Authors: | Greenberg, L.R, Walsh, M.E, Kazlauskas, R.J, Pierce, C.T, Shi, K, Aihara, H, Evans, R.L. | Deposit date: | 2022-10-19 | Release date: | 2022-11-30 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | to be published 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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5WLY
| E. coli LpxH- 8 mutations | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, FORMIC ACID, ... | Authors: | Bohl, T.E, Aihara, H, Shi, K, Lee, J.K. | Deposit date: | 2017-07-28 | Release date: | 2018-04-11 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J. Biol. Chem., 293, 2018
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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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7S6T
| Complex structure of Methane monooxygenase hydroxylase and regulatory subunit H33A | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | Authors: | Johns, J.C, Banerjee, R, Semonis, M.M, Shi, K, Aihara, H, Lipscomb, J.D. | Deposit date: | 2021-09-14 | Release date: | 2021-12-29 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.82 Å) | Cite: | X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry, 61, 2022
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7S6S
| Complex structure of Methane monooxygenase hydroxylase and regulatory subunit DBL1 | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | Authors: | Johns, J.C, Banerjee, R, Semonis, M.M, Shi, K, Aihara, H, Lipscomb, J.D. | Deposit date: | 2021-09-14 | Release date: | 2021-12-29 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry, 61, 2022
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7S6R
| Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with H5A mutation | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | Authors: | Johns, J.C, Banerjee, R, Semonis, M.M, Shi, K, Aihara, H, Lipscomb, J.D. | Deposit date: | 2021-09-14 | Release date: | 2021-12-29 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry, 61, 2022
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7S6Q
| Complex structure of Methane monooxygenase hydroxylase and regulatory subunit DBL2 | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | Authors: | Johns, J.C, Banerjee, R, Semonis, M.M, Shi, K, Aihara, H, Lipscomb, J.D. | Deposit date: | 2021-09-14 | Release date: | 2021-12-29 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry, 61, 2022
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7S7H
| Complex structure of Methane monooxygenase hydroxylase and regulatory subunit DBL2 | Descriptor: | 1,2-ETHANEDIOL, FE (III) ION, Methane monooxygenase beta chain, ... | Authors: | Johns, J.C, Banerjee, R, Semonis, M.M, Shi, K, Aihara, H, Lipscomb, J.D. | Deposit date: | 2021-09-16 | Release date: | 2021-12-29 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics. Biochemistry, 61, 2022
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7TGR
| Structure of SARS-CoV-2 main protease in complex with GC376 | Descriptor: | (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 1,2-ETHANEDIOL, ... | Authors: | Esler, M.A, Shi, K, Aihara, H, Harris, R.S. | Deposit date: | 2022-01-09 | Release date: | 2022-05-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.68 Å) | Cite: | Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro /3CL pro in Living Cells. Mbio, 13, 2022
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7U0N
| Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human 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: | Geng, Q, Shi, K, Ye, G, Zhang, W, Aihara, H, Li, F. | Deposit date: | 2022-02-18 | Release date: | 2022-03-30 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.61 Å) | Cite: | Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1. J.Virol., 96, 2022
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7UFL
| Crystal structure of chimeric omicron RBD (strain BA.2) complexed with chimeric mouse 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: | Zhang, W, Shi, K, Geng, Q, Ye, G, Aihara, H, Li, F. | Deposit date: | 2022-03-22 | Release date: | 2022-10-19 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.84 Å) | Cite: | Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Proc.Natl.Acad.Sci.USA, 119, 2022
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7UFK
| Crystal structure of chimeric omicron RBD (strain BA.2) complexed with human 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: | Zhang, W, Shi, K, Geng, Q, Ye, G, Aihara, H, Li, F. | Deposit date: | 2022-03-22 | Release date: | 2022-10-19 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.38 Å) | Cite: | Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Proc.Natl.Acad.Sci.USA, 119, 2022
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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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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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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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3HL6
| Staphylococcus aureus pathogenicity island 3 ORF9 protein | Descriptor: | CHLORIDE ION, Pathogenicity island protein | Authors: | Kruse, A.C, Huseby, M, Shi, K, Digre, J, Schlievert, P.M, Ohlendorf, D.H, Earhart, C.A. | Deposit date: | 2009-05-26 | Release date: | 2010-06-09 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural and functional studies of a pathogenicity island protein from Staphylococcus aureus To be Published
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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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