6DUQ
 
 | | Structure of a Rho-NusG KOW domain complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, MAGNESIUM ION, ... | | Authors: | Berger, J.M, Lawson, M.R. | | Deposit date: | 2018-06-21 | | Release date: | 2018-09-05 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein.
Mol. Cell, 71, 2018
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1BGW
 | | TOPOISOMERASE RESIDUES 410-1202, | | Descriptor: | TOPOISOMERASE | | Authors: | Berger, J.M, Gamblin, S.J, Harrison, S.C, Wang, J.C. | | Deposit date: | 1996-02-20 | | Release date: | 1996-07-11 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structure and mechanism of DNA topoisomerase II.
Nature, 379, 1996
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7MU5
 | | Human DCTPP1 bound to Triptolide | | Descriptor: | MAGNESIUM ION, dCTP pyrophosphatase 1, triptolide | | Authors: | Hauk, G, Berger, J.M. | | Deposit date: | 2021-05-14 | | Release date: | 2022-08-24 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance
To Be Published
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1VS0
 | | Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A | | Descriptor: | CHLORIDE ION, MAGNESIUM ION, Putative DNA ligase-like protein Rv0938/MT0965, ... | | Authors: | Akey, D, Martins, A, Aniukwu, J, Glickman, M.S, Shuman, S, Berger, J.M, TB Structural Genomics Consortium (TBSGC) | | Deposit date: | 2006-01-27 | | Release date: | 2006-02-28 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal Structure and Nonhomologous End-joining Function of the Ligase Component of Mycobacterium DNA Ligase D.
J.Biol.Chem., 281, 2006
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4FM9
 | | Human topoisomerase II alpha bound to DNA | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3'), DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'), DNA topoisomerase 2-alpha, ... | | Authors: | Wendorff, T.J, Schmidt, B.H, Heslop, P, Austin, C.A, Berger, J.M. | | Deposit date: | 2012-06-15 | | Release date: | 2012-08-08 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.901 Å) | | Cite: | The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage.
J.Mol.Biol., 424, 2012
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3UC1
 | | Mycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain | | Descriptor: | ACETATE ION, CALCIUM ION, DNA gyrase subunit A, ... | | Authors: | Tretter, E.M, Berger, J.M. | | Deposit date: | 2011-10-25 | | Release date: | 2012-03-28 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Mechanisms for Defining Supercoiling Set Point of DNA Gyrase Orthologs: II. THE SHAPE OF THE GyrA SUBUNIT C-TERMINAL DOMAIN (CTD) IS NOT A SOLE DETERMINANT FOR CONTROLLING SUPERCOILING EFFICIENCY.
J.Biol.Chem., 287, 2012
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5HE9
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7UGW
 | | M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin | | Descriptor: | DNA (46-MER), DNA gyrase subunit A, DNA gyrase subunit B, ... | | Authors: | Hauk, G, Imai, Y, Lewis, K, Berger, J.M. | | Deposit date: | 2022-03-25 | | Release date: | 2022-08-17 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis.
Nat.Chem.Biol., 18, 2022
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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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4TY0
 | | Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear intermediate 5' pppA(3',5')pG | | Descriptor: | ACETATE ION, Cyclic AMP-GMP synthase, MAGNESIUM ION, ... | | Authors: | Kranzusch, P.J, Lee, A.S.Y, Wilson, S.C, Solovykh, M.S, Vance, R.E, Berger, J.M, Doudna, J.A. | | Deposit date: | 2014-07-07 | | Release date: | 2014-08-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.
Cell, 158, 2014
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4TXZ
 | | Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with nonhydrolyzable GTP | | Descriptor: | Cyclic AMP-GMP synthase, MAGNESIUM ION, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER | | Authors: | Kranzusch, P.J, Lee, A.S.Y, Wilson, S.C, Solovykh, M.S, Vance, R.E, Berger, J.M, Doudna, J.A. | | Deposit date: | 2014-07-07 | | Release date: | 2014-08-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.
Cell, 158, 2014
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3C4O
 | | Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M/S130K/S146M complex | | Descriptor: | Beta-lactamase SHV-1, Beta-lactamase inhibitory protein, SULFATE ION | | Authors: | Reynolds, K.A, Hanes, M.S, Thomson, J.M, Antczak, A.J, Berger, J.M, Bonomo, R.A, Kirsch, J.F, Handel, T.M. | | Deposit date: | 2008-01-30 | | Release date: | 2008-05-27 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface.
J.Mol.Biol., 382, 2008
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3C4P
 | | Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M complex | | Descriptor: | Beta-lactamase SHV-1, Beta-lactamase inhibitory protein, SULFATE ION | | Authors: | Reynolds, K.A, Hanes, M.S, Thomson, J.M, Antczak, A.J, Berger, J.M, Bonomo, R.A, Kirsch, J.F, Handel, T.M. | | Deposit date: | 2008-01-30 | | Release date: | 2008-05-27 | | Last modified: | 2021-10-20 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface.
J.Mol.Biol., 382, 2008
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4GFH
 | | Topoisomerase II-DNA-AMPPNP complex | | Descriptor: | 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'), DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3'), ... | | Authors: | Schmidt, B.H, Osheroff, N, Berger, J.M. | | Deposit date: | 2012-08-03 | | Release date: | 2012-10-03 | | Last modified: | 2019-07-31 | | Method: | X-RAY DIFFRACTION (4.408 Å) | | Cite: | Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
Nat.Struct.Mol.Biol., 19, 2012
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8TXR
 | | E. coli ExoVII(H238A) | | Descriptor: | Exodeoxyribonuclease 7 large subunit, Exodeoxyribonuclease 7 small subunit | | Authors: | Liu, C, Berger, J.M. | | Deposit date: | 2023-08-24 | | Release date: | 2024-01-31 | | Last modified: | 2024-02-07 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structure of Escherichia coli exonuclease VII.
Proc.Natl.Acad.Sci.USA, 121, 2024
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1BJT
 | | TOPOISOMERASE II RESIDUES 409-1201 | | Descriptor: | TOPOISOMERASE II | | Authors: | Fass, D, Bogden, C.E, Berger, J.M. | | Deposit date: | 1998-06-29 | | Release date: | 1999-05-04 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.
Nat.Struct.Biol., 6, 1999
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6U0W
 | | Crystal structure of Staphylococcal nuclease variant Delta+PHS K133M at cryogenic temperature | | Descriptor: | CALCIUM ION, THYMIDINE-3',5'-DIPHOSPHATE, Thermonuclease | | Authors: | Jeliazkov, J.R, Robinson, A.C, Berger, J.M, Garcia-Moreno E, B, Gray, J.G. | | Deposit date: | 2019-08-15 | | Release date: | 2019-08-28 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Toward the computational design of protein crystals with improved resolution.
Acta Crystallogr D Struct Biol, 75, 2019
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6OK8
 | | Crystal structure of Staphylococcal nuclease variant Delta+PHS K127L at cryogenic temperature | | Descriptor: | CALCIUM ION, THYMIDINE-3',5'-DIPHOSPHATE, Thermonuclease | | Authors: | Jeliazkov, J.R, Robinson, A.C, Berger, J.M, Garcia-Moreno E, B, Gray, J.G. | | Deposit date: | 2019-04-12 | | Release date: | 2019-05-08 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Toward the computational design of protein crystals with improved resolution.
Acta Crystallogr D Struct Biol, 75, 2019
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6U0X
 | | Crystal structure of Staphylococcal nuclease variant Delta+PHS Q123D at cryogenic temperature | | Descriptor: | CALCIUM ION, THYMIDINE-3',5'-DIPHOSPHATE, Thermonuclease | | Authors: | Jeliazkov, J.R, Robinson, A.C, Berger, J.M, Garcia-Moreno E, B, Gray, J.G. | | Deposit date: | 2019-08-15 | | Release date: | 2019-08-28 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Toward the computational design of protein crystals with improved resolution.
Acta Crystallogr D Struct Biol, 75, 2019
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6QEL
 | | E. coli DnaBC apo complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA replication protein dnaC, MAGNESIUM ION, ... | | Authors: | Arias-Palomo, E, Puri, N, O'Shea Murray, V.L, Yan, Q, Berger, J.M. | | Deposit date: | 2019-01-08 | | Release date: | 2019-03-06 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA.
Mol.Cell, 74, 2019
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6QEM
 | | E. coli DnaBC complex bound to ssDNA | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA replication protein DnaC, MAGNESIUM ION, ... | | Authors: | Arias-Palomo, E, Puri, N, O'Shea Murray, V.L, Yan, Q, Berger, J.M. | | Deposit date: | 2019-01-08 | | Release date: | 2019-03-06 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA.
Mol.Cell, 74, 2019
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4TMA
 | | Crystal structure of gyrase bound to its inhibitor YacG | | Descriptor: | DNA gyrase inhibitor YacG, DNA gyrase subunit A, DNA gyrase subunit B, ... | | Authors: | Vos, S.M, Lyubimov, A.Y, Hershey, D.M, Schoeffler, A.J, Berger, J.M. | | Deposit date: | 2014-05-31 | | Release date: | 2014-07-23 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein.
Genes Dev., 28, 2014
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4NMN
 | | Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Replicative DNA helicase, ... | | Authors: | Lyubimov, A.Y, Strycharska, M.S, Erzberger, J.P, Berger, J.M. | | Deposit date: | 2013-11-15 | | Release date: | 2014-01-29 | | Method: | X-RAY DIFFRACTION (3.301 Å) | | Cite: | Nucleotide and partner-protein control of bacterial replicative helicase structure and function.
Mol.Cell, 52, 2013
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4TXY
 | | Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase, a prokaryotic cGAS homolog | | Descriptor: | Cyclic AMP-GMP synthase, MAGNESIUM ION | | Authors: | Kranzusch, P.J, Lee, A.S.Y, Wilson, S.C, Solovykh, M.S, Vance, R.E, Berger, J.M, Doudna, J.A. | | Deposit date: | 2014-07-07 | | Release date: | 2014-08-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (3.0001 Å) | | Cite: | Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.
Cell, 158, 2014
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