PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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1O3R	PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Descriptor: 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3', 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3', ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, ... Authors: Chen, S, Vojtechovsky, J, Parkinson, G.N, Ebright, R.H, Berman, H.M. Deposit date: 2003-03-18 Release date: 2003-04-08 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (3 Å) Cite: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking J.Mol.Biol., 314, 2001
1O3T	PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Descriptor: 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*G)-3', 5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3', ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, ... Authors: Chen, S, Vojtechovsky, J, Parkinson, G.N, Ebright, R.H, Berman, H.M. Deposit date: 2003-03-18 Release date: 2003-04-08 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking J.Mol.Biol., 314, 2001
8XRF	The crystal structure of AsfvTopII in complex with G-DNA Descriptor: DNA (52-MER), DNA topoisomerase 2, MAGNESIUM ION Authors: Yang, J, Gan, J.H. Deposit date: 2024-01-07 Release date: 2024-08-07 Method: X-RAY DIFFRACTION (2.94 Å) Cite: The crystal structure of AsfvTopII in complex with G-DNA Nat Commun, 2024
6UQ3	RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 5 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.47 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6UPX	RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 1 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.4 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6UQ2	RNA polymerase II elongation complex with dG in state 1 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.2 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6UQ0	RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 4 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (3.56 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6UQ1	RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 6 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (3.6 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6BLO	Pol II elongation complex with an abasic lesion at i+1 position Descriptor: DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-10 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.401 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
4XBA	Hnt3 Descriptor: Aprataxin-like protein, GLYCEROL, GUANOSINE, ... Authors: Jacewicz, A, Chauleau, M, Shuman, S. Deposit date: 2014-12-16 Release date: 2015-06-03 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.5 Å) Cite: DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition. Nucleic Acids Res., 43, 2015
6MRJ	Crystal structure of H.pylori NikR in complex with DNA Descriptor: DNA (36-MER), MAGNESIUM ION, NICKEL (II) ION, ... Authors: Pozharski, E, de Serrano, V. Deposit date: 2018-10-13 Release date: 2019-11-20 Last modified: 2023-10-11 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Crystal structure of H.pylori NikR in complex with DNA To Be Published
6BM2	Pol II elongation complex with an abasic lesion at i-1 position Descriptor: DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-13 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.403 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
1EXJ	CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPP Descriptor: DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3'), MULTIDRUG-EFFLUX TRANSPORTER REGULATOR, SODIUM ION, ... Authors: Zheleznova-Heldwein, E.E, Brennan, R.G. Deposit date: 2000-05-02 Release date: 2001-01-24 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (3 Å) Cite: Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature, 409, 2001
1EXI	CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB Descriptor: DNA (5'-D(*AP*CP*CP*CP*TP*CP*CP*CP*CP*TP*TP*AP*GP*GP*GP*GP*AP*GP*GP*GP*T)-3'), MULTIDRUG-EFFLUX TRANSPORTER REGULATOR, TETRAPHENYLANTIMONIUM ION, ... Authors: Zheleznova-Heldwein, E.E, Brennan, R.G. Deposit date: 2000-05-02 Release date: 2001-01-24 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (3.12 Å) Cite: Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature, 409, 2001
6UPZ	RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3 Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... Authors: Oh, J, Wang, D. Deposit date: 2019-10-18 Release date: 2020-06-10 Last modified: 2024-10-16 Method: X-RAY DIFFRACTION (3.1 Å) Cite: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
6BQF	Pol II elongation complex with 'dT-AP' at i+1, i-1 position Descriptor: DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... Authors: Wang, W, Wang, D. Deposit date: 2017-11-27 Release date: 2018-02-28 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (3.35 Å) Cite: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
1O3S	PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Descriptor: 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3', 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3', ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, ... Authors: Chen, S, Ebright, R.H, Berman, H.M. Deposit date: 2003-03-18 Release date: 2003-04-08 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (3 Å) Cite: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking J.Mol.Biol., 314, 2001
9BH7	Human DNA polymerase theta helicase domain dimer in the apo form Descriptor: DNA polymerase theta Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair To Be Published
9BH6	Human DNA polymerase theta helicase domain tetramer in the apo form Descriptor: DNA polymerase theta Authors: Zerio, C.J, Lander, G.C. Deposit date: 2024-04-19 Release date: 2024-05-01 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Human polymerase theta helicase positions DNA microhomologies for double-strand break repair To Be Published
5JU7	DNA BINDING DOMAIN OF E.COLI CADC Descriptor: Transcriptional activator CadC, ZINC ION Authors: Janowski, R, Schlundt, A, Sattler, M, Niessing, D. Deposit date: 2016-05-10 Release date: 2017-04-26 Last modified: 2024-05-08 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator. Sci Rep, 7, 2017
8Y2I	Ternary structure of dLesCas12e-sgRNA-dsDNA Descriptor: DNA (35-MER), dLesCas12e, sgRNA Authors: Zhang, S, Lin, S, Liu, J.J.G. Deposit date: 2024-01-26 Release date: 2024-10-23 Method: ELECTRON MICROSCOPY (2.92 Å) Cite: Ternary structure of dVemCas12e-sgRNA-dsDNA To Be Published
1KOY	NMR structure of DFF-C domain Descriptor: DNA fragmentation factor alpha subunit Authors: Fukushima, K, Kikuchi, J, Koshiba, S, Kigawa, T, Kuroda, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2001-12-25 Release date: 2002-09-04 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation. J.Mol.Biol., 321, 2002
4WXX	The crystal structure of human DNMT1(351-1600) Descriptor: DNA (cytosine-5)-methyltransferase 1, S-ADENOSYL-L-HOMOCYSTEINE, ZINC ION Authors: Zhang, Z.M, Song, J. Deposit date: 2014-11-14 Release date: 2015-07-15 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.622 Å) Cite: Crystal Structure of Human DNA Methyltransferase 1. J.Mol.Biol., 427, 2015
1PNR	PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX Descriptor: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3'), HYPOXANTHINE, PROTEIN (PURINE REPRESSOR) Authors: Schumacher, M.A, Choi, K.Y, Zalkin, H, Brennan, R.G. Deposit date: 1995-03-29 Release date: 1995-11-20 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science, 266, 1994
1FLI	DNA-BINDING DOMAIN OF FLI-1 Descriptor: FLI-1 Authors: Liang, H, Mao, X, Olejniczak, E.T, Nettesheim, D.G, Yu, L, Meadows, R.P, Thompson, C.B, Fesik, S.W. Deposit date: 1994-09-15 Release date: 1995-09-15 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Solution structure of the ets domain of Fli-1 when bound to DNA. Nat.Struct.Biol., 1, 1994

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