PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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4OWW	Structural basis of SOSS1 in complex with a 35nt ssDNA Descriptor: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3'), Integrator complex subunit 3, SOSS complex subunit B1, ... Authors: Ren, W, Sun, Q, Tang, X, Song, H. Deposit date: 2014-02-04 Release date: 2014-04-16 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Structural Basis of SOSS1 Complex Assembly and Recognition of ssDNA. Cell Rep, 6, 2014
7D98	Crystal structure of full-length CbnR complexed with the target DNA complex Descriptor: DNA (56-mer), LysR-type regulatory protein Authors: Senda, M, Giannopoulou, E, Senda, T. Deposit date: 2020-10-12 Release date: 2021-03-10 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (3.6 Å) Cite: Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA. Febs J., 288, 2021
4SKN	A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA Descriptor: DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3'), PROTEIN (URACIL-DNA GLYCOSYLASE), ... Authors: Slupphaug, G, Mol, C.D, Kavli, B, Arvai, A.S, Krokan, H.E, Tainer, J.A. Deposit date: 1999-02-20 Release date: 1999-02-26 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.9 Å) Cite: A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature, 384, 1996
1VKX	CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA Descriptor: DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)-3'), DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)-3'), PROTEIN (NF-KAPPA B P50 SUBUNIT), ... Authors: Chen, F, Huang, D.B, Ghosh, G. Deposit date: 1997-09-17 Release date: 1998-12-09 Last modified: 2024-10-16 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature, 391, 1998
5H3R	Crystal Structure of mutant MarR C80S from E.coli complexed with operator DNA Descriptor: DNA (5'-D(*CP*AP*TP*AP*CP*TP*TP*GP*CP*CP*TP*GP*GP*GP*CP*AP*AP*TP*AP*TP*T)-3'), DNA (5'-D(*GP*AP*AP*TP*AP*TP*TP*GP*CP*CP*CP*AP*GP*GP*CP*AP*AP*GP*TP*AP*T)-3'), Multiple antibiotic resistance protein MarR Authors: Zhu, R, Lou, H, Hao, Z. Deposit date: 2016-10-26 Release date: 2017-08-02 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.67 Å) Cite: Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator. J. Biol. Inorg. Chem., 22, 2017
1BY4	STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA Descriptor: DNA (5'-D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3'), PROTEIN (RETINOIC ACID RECEPTOR RXR-ALPHA), ... Authors: Zhao, Q, Chasse, S.A, Devarakonda, S, Sierk, M.L, Ahvazi, B, Sigler, P.B, Rastinejad, F. Deposit date: 1998-10-22 Release date: 2000-01-12 Last modified: 2023-08-09 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Structural basis of RXR-DNA interactions. J.Mol.Biol., 296, 2000
5FKU	cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex) Descriptor: DNA POLYMERASE III SUBUNIT ALPHA, DNA POLYMERASE III SUBUNIT BETA, DNA POLYMERASE III SUBUNIT EPSILON, ... Authors: Fernandez-Leiro, R, Conrad, J, Scheres, S.H.W, Lamers, M.H. Deposit date: 2015-10-20 Release date: 2015-11-25 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (8.34 Å) Cite: cryo-EM structures of theE. colireplicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease andtau. Elife, 4, 2015
4LJL	Structural insights into the unique single-stranded DNA binding mode of DNA processing protein A from Helicobacter pylori Descriptor: DNA processing chain A (DprA) Authors: Wang, W. Deposit date: 2013-07-05 Release date: 2014-01-01 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. Nucleic Acids Res., 42, 2014
4LJK	Structural insights into the unique single-stranded DNA binding mode of DNA processing protein A from Helicobacter pylori Descriptor: DNA processing chain A (DprA) Authors: Wang, W. Deposit date: 2013-07-05 Release date: 2014-01-01 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.354 Å) Cite: Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. Nucleic Acids Res., 42, 2014
3U6Y	Crystal structure of ALBA2-DNA complex Descriptor: DNA (5'-D(*CP*CP*GP*GP*C)-3'), DNA (5'-D(*GP*GP*CP*CP*G)-3'), DNA/RNA-binding protein Alba 2, ... Authors: Kumarevel, T, Tanaka, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2011-10-13 Release date: 2012-02-22 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2 Å) Cite: Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1. J.Biol.Chem., 287, 2012
7T22	E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Descriptor: ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), DNA primase, ... Authors: Oakley, A.J, Xu, Z.Q. Deposit date: 2021-12-02 Release date: 2023-01-18 Last modified: 2024-10-16 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli To Be Published
1EN9	1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM. Descriptor: DNA (5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3'), MAGNESIUM ION Authors: Chiu, T.K, Dickerson, R.E. Deposit date: 2000-03-20 Release date: 2000-09-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (0.985 Å) Cite: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J.Mol.Biol., 301, 2000
2STW	SOLUTION NMR STRUCTURE OF THE HUMAN ETS1/DNA COMPLEX, RESTRAINED REGULARIZED MEAN STRUCTURE Descriptor: DNA (5'-D(*TP*CP*GP*AP*AP*CP*TP*TP*CP*CP*GP*GP*CP*TP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*AP*GP*CP*CP*GP*GP*AP*AP*GP*TP*TP*CP*GP*A)-3'), ETS1 Authors: Clore, G.M, Werner, M.H, Gronenborn, A.M. Deposit date: 1996-08-05 Release date: 1997-03-12 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: Correction of the NMR structure of the ETS1/DNA complex. J.Biomol.NMR, 10, 1997
7PC6	DNA-binding domain of a p53 homolog from the hydrothermal vent annelid Alvinella pompejana Descriptor: 1,2-ETHANEDIOL, DNA-binding domain, ZINC ION Authors: Balourdas, D.-I, Knapp, S, Soussi, T, Joerger, A.C, Structural Genomics Consortium (SGC) Deposit date: 2021-08-03 Release date: 2022-03-23 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (1.92 Å) Cite: Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog. Cell Death Dis, 13, 2022
1EN3	1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM Descriptor: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3'), MAGNESIUM ION Authors: Chiu, T.K, Dickerson, R.E. Deposit date: 2000-03-20 Release date: 2000-09-25 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (0.985 Å) Cite: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J.Mol.Biol., 301, 2000
1B72	PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX Descriptor: DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3'), DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3'), PROTEIN (HOMEOBOX PROTEIN HOX-B1), ... Authors: Piper, D.E, Batchelor, A.H, Chang, C.-P, Cleary, M.L, Wolberger, C. Deposit date: 1999-01-27 Release date: 1999-02-19 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.35 Å) Cite: Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation. Cell(Cambridge,Mass.), 96, 1999
7VUP	Structure of NF-kB p52 homodimer bound to +1/-1 swap P-Selectin kB DNA fragment Descriptor: DNA (5'-D(*AP*AP*GP*GP*GP*GP*GP*AP*GP*TP*CP*CP*CP*CP*TP*TP*G)-3'), DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*AP*CP*TP*CP*CP*CP*CP*CP*TP*T)-3'), Nuclear factor NF-kappa-B p52 subunit Authors: Meshcheryakov, V.A, Wang, V.Y.-F. Deposit date: 2021-11-04 Release date: 2021-11-24 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. Elife, 12, 2023
7VUQ	Structure of NF-kB p52 homodimer bound to A/T-centric P-Selectin kB DNA fragment Descriptor: DNA (5'-D(*CP*AP*AP*GP*GP*GP*GP*TP*TP*AP*CP*CP*CP*CP*CP*TP*T)-3'), DNA (5'-D(*GP*AP*AP*GP*GP*GP*GP*GP*TP*AP*AP*CP*CP*CP*CP*TP*TP*G)-3'), Nuclear factor NF-kappa-B p52 subunit Authors: Meshcheryakov, V.A, Wang, V.Y.-F. Deposit date: 2021-11-04 Release date: 2021-11-24 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. Elife, 12, 2023
1AZQ	HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX Descriptor: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3'), PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D) Authors: Robinson, H, Gao, Y.-G, Mccrary, B.S, Edmondson, S.P, Shriver, J.W, Wang, A.H.-J. Deposit date: 1997-11-20 Release date: 1999-01-13 Last modified: 2023-08-02 Method: X-RAY DIFFRACTION (1.94 Å) Cite: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 1998
1AZP	HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX Descriptor: DNA (5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'), PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D) Authors: Robinson, H, Gao, Y.-G, Mccrary, B.S, Edmondson, S.P, Shriver, J.W, Wang, A.H.-J. Deposit date: 1997-11-19 Release date: 1999-01-13 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (1.6 Å) Cite: The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 1998
1YSA	THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX Descriptor: DNA (5'-D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3'), DNA (5'-D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3'), PROTEIN (GCN4) Authors: Ellenberger, T.E, Brandl, C.J, Struhl, K, Harrison, S.C. Deposit date: 1993-08-09 Release date: 1993-10-31 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (2.9 Å) Cite: The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell(Cambridge,Mass.), 71, 1992
4QJU	Crystal structure of DNA-bound nucleoid associated protein, SAV1473 Descriptor: DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'), DNA-binding protein HU Authors: Lee, B.-J, Kim, D.-H, Im, H, Yoon, H.-J. Deposit date: 2014-06-04 Release date: 2014-12-17 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.16 Å) Cite: beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism Acta Crystallogr.,Sect.D, 70, 2014
1D87	CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES Descriptor: DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3') Authors: Egli, M, Usman, N, Rich, A. Deposit date: 1992-08-28 Release date: 1993-07-15 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Biochemistry, 32, 1993
6RKW	CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex Descriptor: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione, DNA (58-MER), DNA (62-MER), ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2019-04-30 Release date: 2019-11-06 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (6.6 Å) Cite: Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun, 10, 2019
6RKS	E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion Descriptor: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione, DNA Strand 1, DNA Strand 2, ... Authors: Vanden Broeck, A, Lamour, V. Deposit date: 2019-04-30 Release date: 2019-11-06 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4 Å) Cite: Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun, 10, 2019

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