1D30
 
 | | THE STRUCTURE OF DAPI BOUND TO DNA | | Descriptor: | 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | | Authors: | Larsen, T, Goodsell, D.S, Cascio, D, Grzeskowiak, K, Dickerson, R.E. | | Deposit date: | 1991-01-04 | | Release date: | 1992-04-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | The structure of DAPI bound to DNA.
J.Biomol.Struct.Dyn., 7, 1989
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3BKZ
 | | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | | Descriptor: | 2-OXOGLUTARIC ACID, Alpha-ketoglutarate-dependent dioxygenase alkB, DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3'), ... | | Authors: | Yi, C, Yang, C.-G, He, C. | | Deposit date: | 2007-12-09 | | Release date: | 2008-04-22 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA
Nature, 452, 2008
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3BTX
 | | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | | Descriptor: | Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3'), DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-3'), ... | | Authors: | Yang, C.-G, Yi, C, He, C. | | Deposit date: | 2007-12-31 | | Release date: | 2008-04-22 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Nature, 452, 2008
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3BU0
 | | crystal structure of human ABH2 cross-linked to dsDNA with cofactors | | Descriptor: | 2-OXOGLUTARIC ACID, Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3'), ... | | Authors: | Yang, C.-G, Yi, C, He, C. | | Deposit date: | 2007-12-31 | | Release date: | 2008-04-22 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Nature, 452, 2008
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6PIJ
 | | Target DNA-bound V. cholerae TniQ-Cascade complex, closed conformation | | Descriptor: | Non-targeting strand ssDNA, Targeting strand ssDNA, TniQ monomer 2, ... | | Authors: | Halpin-Healy, T, Klompe, S, Sternberg, S.H. | | Deposit date: | 2019-06-26 | | Release date: | 2019-10-02 | | Last modified: | 2024-03-20 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system.
Nature, 577, 2020
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3L4J
 | | Topoisomerase II-DNA cleavage complex, apo | | Descriptor: | 3'-THIO-THYMIDINE-5'-PHOSPHATE, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3'), DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3'), ... | | Authors: | Schmidt, B.H, Burgin, A.B, Deweese, J.E, Osheroff, N, Berger, J.M. | | Deposit date: | 2009-12-20 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.48 Å) | | Cite: | A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
Nature, 465, 2010
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3L4K
 | | Topoisomerase II-DNA cleavage complex, metal-bound | | Descriptor: | 3'-THIO-THYMIDINE-5'-PHOSPHATE, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3'), DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3'), ... | | Authors: | Schmidt, B.H, Burgin, A.B, Deweese, J.E, Osheroff, N, Berger, J.M. | | Deposit date: | 2009-12-20 | | Release date: | 2010-05-26 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.98 Å) | | Cite: | A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
Nature, 465, 2010
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8KAK
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8KAJ
 | | Crystal structure of SpyCas9-crRNA-tracrRNA complex bound to 16nt target DNA | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*CP*AP*AP*TP*AP*CP*CP*TP*TP*TP*TP*AP*TP*CP*CP*AP*TP*AP*AP*AP*TP*TP*CP*G)-3'), DNA (5'-D(*TP*TP*TP*AP*GP*GP*TP*AP*TP*TP*G)-3'), ... | | Authors: | Chen, Y, Chen, J, Liu, L. | | Deposit date: | 2023-08-03 | | Release date: | 2024-06-05 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (3.42 Å) | | Cite: | Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
Nat.Biotechnol., 2024
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8KAI
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8KAH
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8KAM
 | | Crystal structure of SpyCas9 in complex with sgRNA and 16nt target DNA | | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, DNA (5'-D(*CP*AP*AP*TP*AP*CP*CP*TP*CP*TP*TP*CP*AP*AP*TP*TP*AP*GP*AP*AP*CP*AP*CP*G)-3'), DNA (5'-D(*TP*TP*TP*AP*GP*GP*TP*AP*TP*TP*G)-3'), ... | | Authors: | Chen, Y, Chen, J, Liu, L. | | Deposit date: | 2023-08-03 | | Release date: | 2024-06-05 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (3.91 Å) | | Cite: | Trans-nuclease activity of Cas9 activated by DNA or RNA target binding.
Nat.Biotechnol., 2024
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8KAL
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7VW3
 | | Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex | | Descriptor: | CRISPR-associated endonuclease Cas9, MAGNESIUM ION, Non-target DNA strand, ... | | Authors: | Du, W.H, Qian, J.Q, Huang, Q. | | Deposit date: | 2021-11-09 | | Release date: | 2023-03-15 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State.
Int J Mol Sci, 24, 2023
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7L4X
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7L4Y
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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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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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8YXX
 | | TRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCG-3') | | Descriptor: | Activating signal cointegrator 1, DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3'), DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*G)-3') | | Authors: | Ding, J, Yang, H, Hu, C. | | Deposit date: | 2024-04-03 | | Release date: | 2024-06-26 | | Last modified: | 2024-08-28 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role.
Structure, 32, 2024
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8YXW
 | | TRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCC-3') | | Descriptor: | Activating signal cointegrator 1, DNA (5'-D(*GP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3'), DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*C)-3') | | Authors: | Ding, J, Yang, H, Hu, C. | | Deposit date: | 2024-04-03 | | Release date: | 2024-06-26 | | Last modified: | 2024-08-28 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role.
Structure, 32, 2024
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6O0X
 | | Conformational states of Cas9-sgRNA-DNA ternary complex in the presence of magnesium | | Descriptor: | 3' product of target strand DNA, 5' product of target strand DNA, CRISPR-associated endonuclease Cas9/Csn1, ... | | Authors: | Zhu, X, Clarke, R, Puppala, A.K, Chittori, S, Merk, A, Merrill, B.J, Simonovic, M, Subramaniam, S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-07-10 | | Last modified: | 2024-03-20 | | Method: | ELECTRON MICROSCOPY (3.28 Å) | | Cite: | Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9.
Nat.Struct.Mol.Biol., 26, 2019
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3BTY
 | | Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site | | Descriptor: | Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2, DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3'), DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3'), ... | | Authors: | Yang, C.-G, Yi, C, He, C. | | Deposit date: | 2007-12-31 | | Release date: | 2008-04-22 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Nature, 452, 2008
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7W5P
 | | Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp N6-methyldeoxyadenine (6mA) containing duplex DNA | | Descriptor: | CcTet, DNA, DNA (12-MER), ... | | Authors: | Mu, Y.J, Zhang, L, Zhang, L. | | Deposit date: | 2021-11-30 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Nat.Chem.Biol., 18, 2022
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8XVC
 | | CryoEM structure of ADP-DNA-MuB conformation1 | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ATP-dependent target DNA activator B | | Authors: | Zhao, X, Zhang, K, Li, S. | | Deposit date: | 2024-01-14 | | Release date: | 2024-08-14 | | Method: | ELECTRON MICROSCOPY (4.32 Å) | | Cite: | Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition.
Nat Commun, 15, 2024
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1O7I
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