2PUE
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![BU of 2pue by Molmil](/molmil-images/mine/2pue) | CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES | Descriptor: | ADENINE, DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3'), PROTEIN (PURINE REPRESSOR ) | Authors: | Lu, F, Schumacher, M.A, Arvidson, D.N, Haldimann, A, Wanner, B.L, Zalkin, H, Brennan, R.G. | Deposit date: | 1997-10-04 | Release date: | 1998-05-06 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190. Biochemistry, 37, 1998
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1L1M
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![BU of 1l1m by Molmil](/molmil-images/mine/1l1m) | SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1 | Descriptor: | 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3', 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3', Lactose operon repressor | Authors: | Kalodimos, C.G, Bonvin, A.M.J.J, Salinas, R.K, Wechselberger, R, Boelens, R, Kaptein, R. | Deposit date: | 2002-02-19 | Release date: | 2002-06-26 | Last modified: | 2021-10-27 | Method: | SOLUTION NMR | Cite: | Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J., 21, 2002
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5FO5
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![BU of 5fo5 by Molmil](/molmil-images/mine/5fo5) | Structure of the DNA-binding domain of Escherichia coli methionine biosynthesis regulator MetR | Descriptor: | 1,2-ETHANEDIOL, HTH-TYPE TRANSCRIPTIONAL REGULATOR METR, MAGNESIUM ION | Authors: | Punekar, A.S, Porter, J, Urbanowski, M.L, Stauffer, G.V, Carr, S.B, Phillips, S.E. | Deposit date: | 2015-11-18 | Release date: | 2016-06-08 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.16 Å) | Cite: | Structural Basis for DNA Recognition by the Transcription Regulator Metr. Acta Crystallogr.,Sect.F, 72, 2016
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8W7S
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![BU of 8w7s by Molmil](/molmil-images/mine/8w7s) | Yeast replisome in state IV | Descriptor: | Cell division control protein 45, DNA (71-mer), DNA polymerase alpha-binding protein, ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D. | Deposit date: | 2023-08-31 | Release date: | 2023-12-20 | Method: | ELECTRON MICROSCOPY (7.39 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
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8W7M
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![BU of 8w7m by Molmil](/molmil-images/mine/8w7m) | Yeast replisome in state V | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cell division control protein 45, DNA (71-mer), ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D, Xu, Z. | Deposit date: | 2023-08-30 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (4.12 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
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4MZ9
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![BU of 4mz9 by Molmil](/molmil-images/mine/4mz9) | Revised structure of E. coli SSB | Descriptor: | Single-stranded DNA-binding protein | Authors: | Oakley, A.J. | Deposit date: | 2013-09-29 | Release date: | 2013-12-18 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy. Nucleic Acids Res., 42, 2014
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1OSL
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![BU of 1osl by Molmil](/molmil-images/mine/1osl) | Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence | Descriptor: | 5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3', Lactose operon repressor | Authors: | Kalodimos, C.G, Bonvin, A.M.J.J, Boelens, R, Kaptein, R. | Deposit date: | 2003-03-20 | Release date: | 2004-05-04 | Last modified: | 2021-10-27 | Method: | SOLUTION NMR | Cite: | Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305, 2004
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1H0M
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![BU of 1h0m by Molmil](/molmil-images/mine/1h0m) | Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA | Descriptor: | 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE, 5'-D(*AP*TP*GP*TP*GP*CP*AP*GP*AP*TP *CP*TP*GP*CP*AP*CP*AP*T)-3', Transcriptional activator protein TraR | Authors: | Vannini, A, Volpari, C, Gargioli, C, Muraglia, E, Cortese, R, De Francesco, R, Neddermann, P, Di Marco, S. | Deposit date: | 2002-06-25 | Release date: | 2002-08-29 | Last modified: | 2020-12-16 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | The Crystal Structure of the Quorum Sensing Protein Trar Bound to its Autoinducer and Target DNA Embo J., 21, 2002
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6LXM
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![BU of 6lxm by Molmil](/molmil-images/mine/6lxm) | Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR as a domain-swapped dimer | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, SULFATE ION, ... | Authors: | Sadotra, S, Chen, C, Hsu, C.H. | Deposit date: | 2020-02-11 | Release date: | 2020-12-23 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.412 Å) | Cite: | Structural basis for promoter DNA recognition by the response regulator OmpR. J.Struct.Biol., 213, 2020
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6LXL
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![BU of 6lxl by Molmil](/molmil-images/mine/6lxl) | |
1GDC
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![BU of 1gdc by Molmil](/molmil-images/mine/1gdc) | REFINED SOLUTION STRUCTURE OF THE GLUCOCORTICOID RECEPTOR DNA-BINDING DOMAIN | Descriptor: | GLUCOCORTICOID RECEPTOR, ZINC ION | Authors: | Baumann, H, Paulsen, K, Kovacs, H, Berglund, H, Wright, A.P.H, Gustafsson, J.-A, Hard, T. | Deposit date: | 1994-03-15 | Release date: | 1994-06-22 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Refined solution structure of the glucocorticoid receptor DNA-binding domain. Biochemistry, 32, 1993
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1O4X
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![BU of 1o4x by Molmil](/molmil-images/mine/1o4x) | |
2Z33
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![BU of 2z33 by Molmil](/molmil-images/mine/2z33) | Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain | Descriptor: | 5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3', 5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3', Phosphate regulon transcriptional regulatory protein phoB | Authors: | Yamane, T, Okamura, H, Ikeguchi, M, Nishimura, Y, Kidera, A. | Deposit date: | 2007-05-31 | Release date: | 2008-04-22 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Proteins, 71, 2008
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3LNQ
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![BU of 3lnq by Molmil](/molmil-images/mine/3lnq) | Structure of Aristaless homeodomain in complex with DNA | Descriptor: | 5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3', 5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3', ACETATE ION, ... | Authors: | Takamura, Y, Miyazono, K, Nagata, K, Saigo, K, Kojima, T, Tanokura, M. | Deposit date: | 2010-02-02 | Release date: | 2010-04-28 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless Embo J., 29, 2010
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8SPQ
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![BU of 8spq by Molmil](/molmil-images/mine/8spq) | SpRY-Cas9:gRNA complex targeting TGG PAM DNA | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, NTS, ... | Authors: | Hibshman, G.N, Bravo, J.P.K, Taylor, D.W. | Deposit date: | 2023-05-03 | Release date: | 2024-05-01 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.26 Å) | Cite: | Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun, 15, 2024
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4A93
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![BU of 4a93 by Molmil](/molmil-images/mine/4a93) | RNA Polymerase II elongation complex containing a CPD Lesion | Descriptor: | 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*T*TTP*TP*TP*CP*C BRUP*GP*GP*TP*CP*AP*TP*T)-3', 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3', 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP*AP)-3', ... | Authors: | Walmacq, C, Cheung, A.C.M, Kireeva, M.L, Lubkowska, L, Ye, C, Gotte, D, Strathern, J.N, Carell, T, Cramer, P, Kashlev, M. | Deposit date: | 2011-11-23 | Release date: | 2012-03-21 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | Mechanism of Translesion Transcription by RNA Polymerase II and its Role in Cellular Resistance to DNA Damage. Mol.Cell, 46, 2012
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1H6F
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![BU of 1h6f by Molmil](/molmil-images/mine/1h6f) | Human TBX3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site | Descriptor: | 5'-D(*TP*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP* AP*GP*GP*TP*GP*TP*GP*AP*AP*AP*T)-3', MAGNESIUM ION, T-BOX TRANSCRIPTION FACTOR TBX3 | Authors: | Coll, M, Muller, C.W. | Deposit date: | 2001-06-13 | Release date: | 2002-04-19 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome Structure, 10, 2002
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1DP7
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![BU of 1dp7 by Molmil](/molmil-images/mine/1dp7) | COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE | Descriptor: | 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3'), ... | Authors: | Gajiwala, K.S, Chen, H, Cornille, F, Roques, B.P, Reith, W, Mach, B, Burley, S.K. | Deposit date: | 1999-12-23 | Release date: | 2000-03-06 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature, 403, 2000
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6PKZ
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![BU of 6pkz by Molmil](/molmil-images/mine/6pkz) | |
6YCQ
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![BU of 6ycq by Molmil](/molmil-images/mine/6ycq) | Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 21-7A, 21-7B, ... | Authors: | Crespo, I, Weijers, D, Boer, D.R. | Deposit date: | 2020-03-18 | Release date: | 2020-09-09 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis . Proc.Natl.Acad.Sci.USA, 117, 2020
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1NWQ
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![BU of 1nwq by Molmil](/molmil-images/mine/1nwq) | CRYSTAL STRUCTURE OF C/EBPALPHA-DNA COMPLEX | Descriptor: | 5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*AP*GP*GP*A)-3', 5'-D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP*TP*T)-3', CCAAT/enhancer binding protein alpha | Authors: | Miller, M, Shuman, J.D, Sebastian, T, Dauter, Z, Johnson, P.F. | Deposit date: | 2003-02-06 | Release date: | 2003-05-13 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Structural Basis for DNA Recognition by the Basic Region Leucine Zipper
Transcription Factor CCAAT/enhancer Binding Protein Alpha J.Biol.Chem., 278, 2003
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4R4E
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![BU of 4r4e by Molmil](/molmil-images/mine/4r4e) | Structure of GlnR-DNA complex | Descriptor: | 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, DNA (5'-D(*AP*TP*TP*CP*TP*GP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*CP*AP*GP*TP*A)-3'), ... | Authors: | Schumacher, M.A. | Deposit date: | 2014-08-19 | Release date: | 2015-03-04 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.57 Å) | Cite: | Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis. Genes Dev., 29, 2015
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8SRS
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![BU of 8srs by Molmil](/molmil-images/mine/8srs) | SpRY-Cas9:gRNA complex targeting TAC PAM DNA | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, NTS, ... | Authors: | Hibshman, G.N, Bravo, J.P.K, Taylor, D.W. | Deposit date: | 2023-05-06 | Release date: | 2024-05-01 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.79 Å) | Cite: | Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun, 15, 2024
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8SQH
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![BU of 8sqh by Molmil](/molmil-images/mine/8sqh) | SpRY-Cas9:gRNA complex targeting TTC PAM DNA | Descriptor: | CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, NTS, ... | Authors: | Hibshman, G.N, Bravo, J.P.K, Taylor, D.W. | Deposit date: | 2023-05-04 | Release date: | 2024-05-01 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.69 Å) | Cite: | Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun, 15, 2024
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1EAQ
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![BU of 1eaq by Molmil](/molmil-images/mine/1eaq) | The RUNX1 Runt domain at 1.25A resolution: A structural switch and specifically bound chloride ions modulate DNA binding | Descriptor: | CHLORIDE ION, RUNT-RELATED TRANSCRIPTION FACTOR 1 | Authors: | Backstrom, S, Wolf-Watz, M, Grundstrom, C, Hard, T, Grundstrom, T, Sauer, U.H. | Deposit date: | 2001-07-14 | Release date: | 2002-09-12 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | The Runx1 Runt Domain at 1.25 A Resolution: A Structural Switch and Specifically Bound Chloride Ions Modulate DNA Binding J.Mol.Biol., 322, 2002
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