6NY1
 
 | | CasX-gRNA-DNA(30bp) State II | | Descriptor: | CasX, DNA Non-target strand, DNA target strand, ... | | Authors: | Liu, J.J, Orlova, N, Nogales, E, Doudna, J.A. | | Deposit date: | 2019-02-10 | | Release date: | 2019-02-27 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | CasX enzymes comprise a distinct family of RNA-guided genome editors.
Nature, 566, 2019
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5NO6
 | | TEAD4-HOXB13 complex bound to DNA | | Descriptor: | DNA, Homeobox protein Hox-B13, Transcriptional enhancer factor TEF-3 | | Authors: | Morgunova, E, Jolma, A, Yin, Y, Popov, A, Taipale, J. | | Deposit date: | 2017-04-11 | | Release date: | 2018-05-16 | | Last modified: | 2025-04-23 | | Method: | X-RAY DIFFRACTION (2.88 Å) | | Cite: | DNA-guided transcription factor interactions extend human gene regulatory code.
Nature, 2025
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5GZB
 | | Crystal Structure of Transcription Factor TEAD4 in Complex with M-CAT DNA | | Descriptor: | DNA (5'-D(*GP*AP*GP*AP*GP*GP*AP*AP*TP*GP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*CP*AP*TP*TP*CP*CP*TP*CP*TP*C)-3'), GLYCEROL, ... | | Authors: | He, F, Shi, Z.B, Zhou, Z.C. | | Deposit date: | 2016-09-28 | | Release date: | 2017-04-19 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.704 Å) | | Cite: | DNA-binding mechanism of the Hippo pathway transcription factor TEAD4
Oncogene, 36, 2017
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5BNG
 | | monomer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA | | Descriptor: | DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3'), DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3'), DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3'), ... | | Authors: | Morgunova, E, Jolma, A, Yin, Y, Nitta, K, Dave, K, Popov, A, Taipale, M, Enge, M, Kivioja, T, Taipale, J. | | Deposit date: | 2015-05-26 | | Release date: | 2015-11-04 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | DNA-dependent formation of transcription factor pairs alters their binding specificity.
Nature, 527, 2015
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4WK8
 | | FOXP3 forms a domain-swapped dimer to bridge DNA | | Descriptor: | DNA (5'-D(*AP*AP*CP*TP*AP*TP*GP*AP*AP*AP*CP*AP*AP*AP*TP*TP*TP*TP*CP*CP*T)-3'), DNA (5'-D(*TP*TP*AP*GP*GP*AP*AP*AP*AP*TP*TP*TP*GP*TP*TP*TP*CP*AP*TP*AP*G)-3'), Forkhead box protein P3 | | Authors: | Chen, Y, Chen, L. | | Deposit date: | 2014-10-01 | | Release date: | 2015-01-21 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (3.4006 Å) | | Cite: | DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
Nucleic Acids Res., 43, 2015
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1D66
 | | DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX | | Descriptor: | CADMIUM ION, DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3'), DNA (5'-D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*TP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3'), ... | | Authors: | Marmorstein, R, Carey, M, Ptashne, M, Harrison, S.C. | | Deposit date: | 1992-03-06 | | Release date: | 1992-03-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | DNA recognition by GAL4: structure of a protein-DNA complex.
Nature, 356, 1992
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4IEM
 | | Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ | | Descriptor: | DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*C)-3'), DNA (5'-D(P*(3DR)P*GP*AP*TP*CP*G)-3'), ... | | Authors: | Tsutakawa, S.E, Mol, C.D, Arvai, A.S, Tainer, J.A. | | Deposit date: | 2012-12-13 | | Release date: | 2013-01-23 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.3936 Å) | | Cite: | Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes.
J.Biol.Chem., 288, 2013
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8OSB
 | | TWIST1-TCF4-ALX4 complex on specific DNA | | Descriptor: | DNA (25-MER), Homeobox protein aristaless-like 4, Transcription factor 4, ... | | Authors: | Morgunova, E, Kim, S, Popov, A, Wysocka, J, Taipale, J. | | Deposit date: | 2023-04-18 | | Release date: | 2024-01-31 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | DNA-guided transcription factor cooperativity shapes face and limb mesenchyme.
Cell, 187, 2024
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1J1V
 | | Crystal structure of DnaA domainIV complexed with DnaAbox DNA | | Descriptor: | 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3', 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3', Chromosomal replication initiator protein dnaA | | Authors: | Fujikawa, N, Kurumizaka, H, Nureki, O, Terada, T, Shirouzu, M, Katayama, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-18 | | Release date: | 2003-04-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis of replication origin recognition by the DnaA protein
NUCLEIC ACIDS RES., 31, 2003
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110D
 | | ANTHRACYCLINE-DNA INTERACTIONS AT UNFAVOURABLE BASE BASE-PAIR TRIPLET-BINDING SITES: STRUCTURES OF D(CGGCCG)/DAUNOMYCIN AND D(TGGCCA)/ADRIAMYCIN COMPL | | Descriptor: | DAUNOMYCIN, DNA (5'-D(*CP*GP*GP*CP*CP*G)-3') | | Authors: | Leonard, G.A, Hambley, T.W, McAuley-Hecht, K, Brown, T, Hunter, W.N. | | Deposit date: | 1993-01-21 | | Release date: | 1993-04-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Anthracycline-DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin complexes.
Acta Crystallogr.,Sect.D, 49, 1993
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1A73
 | | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | | Descriptor: | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON 3 (I-PPO) ENCODED ENDONUCLEASE, ... | | Authors: | Flick, K.E, Monnat Junior, R.J, Stoddard, B.L. | | Deposit date: | 1998-03-19 | | Release date: | 1998-10-14 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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4Z3C
 | | Zinc finger region of human TET3 in complex with CpG DNA | | Descriptor: | DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3'), Methylcytosine dioxygenase, UNKNOWN ATOM OR ION, ... | | Authors: | Liu, K, Xu, C, Tempel, W, Dong, A, Arrowsmith, C.H, Bountra, C, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC) | | Deposit date: | 2015-03-31 | | Release date: | 2015-04-29 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Structure, 2017
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1A74
 | | I-PPOL HOMING ENDONUCLEASE/DNA COMPLEX | | Descriptor: | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*A P*GP*TP*CP*A)-3'), INTRON-ENCODED ENDONUCLEASE I-PPOI, ZINC ION | | Authors: | Jurica, B.L, Flick, K.E, Monnat Junior, R.J, Stoddard, M.S. | | Deposit date: | 1998-03-19 | | Release date: | 1998-06-22 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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5C53
 | | Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma | | Descriptor: | 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE, DNA (26-MER), DNA (5'-D(*AP*AP*AP*AP*CP*GP*AP*GP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*GP*TP*AP*C)-3'), ... | | Authors: | Sohl, C.D, Szymanski, M.R, Mislak, A.C, Shumate, C.K, Amiralaei, S, Schinazi, R.F, Anderson, K.S, Yin, Y.W. | | Deposit date: | 2015-06-19 | | Release date: | 2016-01-27 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (3.567 Å) | | Cite: | Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
Proc.Natl.Acad.Sci.USA, 112, 2015
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5YUR
 | | DNA polymerase IV - DNA ternary complex 1 | | Descriptor: | DNA polymerase IV, DTN, SODIUM ION, ... | | Authors: | Kottur, J, Nair, D.T. | | Deposit date: | 2017-11-23 | | Release date: | 2018-08-29 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.035 Å) | | Cite: | Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Nucleic Acids Res., 46, 2018
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154D
 | | DNA DISTORTION IN BIS-INTERCALATED COMPLEXES | | Descriptor: | BIS-(N-ETHYLPYRIDINIUM-(3-METHOXYCARBAZOLE))HEXANE-1,6-DIAMINE, DNA (5'-D(*(CBR)P*GP*CP*G)-3') | | Authors: | Peek, M.E, Lipscomb, L.A, Bertrand, J.A, Gao, Q, Roques, B.P, Garbay-Jaureguiberry, C, Williams, L.D. | | Deposit date: | 1993-12-14 | | Release date: | 1994-08-31 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | DNA distortion in bis-intercalated complexes.
Biochemistry, 33, 1994
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5YUT
 | | DNA polymerase IV - DNA ternary complex 3 | | Descriptor: | DNA polymerase IV, DTN, MAGNESIUM ION, ... | | Authors: | Kottur, J, Nair, D.T. | | Deposit date: | 2017-11-23 | | Release date: | 2018-09-05 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Nucleic Acids Res., 46, 2018
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5YUU
 | | DNA polymerase IV - DNA ternary complex 4 | | Descriptor: | DNA polymerase IV, DTN1, DTN2, ... | | Authors: | Kottur, J, Nair, D.T. | | Deposit date: | 2017-11-23 | | Release date: | 2019-01-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.892 Å) | | Cite: | Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Nucleic Acids Res., 46, 2018
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5YUS
 | | DNA polymerase IV - DNA ternary complex 2 | | Descriptor: | DNA polymerase IV, DTN, MAGNESIUM ION, ... | | Authors: | Kottur, J, Nair, D.T. | | Deposit date: | 2017-11-23 | | Release date: | 2018-11-07 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Nucleic Acids Res., 46, 2018
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5YUV
 | | DNA polymerase IV - DNA ternary complex 5 | | Descriptor: | DNA polymerase IV, DTN1, DTN2, ... | | Authors: | Kottur, J, Nair, D.T. | | Deposit date: | 2017-11-23 | | Release date: | 2018-10-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Nucleic Acids Res., 46, 2018
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4PZI
 | | Zinc finger region of MLL2 in complex with CpG DNA | | Descriptor: | DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3'), Histone-lysine N-methyltransferase 2B, UNKNOWN ATOM OR ION, ... | | Authors: | Chao, X, Tempel, W, Liu, K, Dong, A, Bountra, C, Weigelt, J, Arrowsmith, C.H, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC) | | Deposit date: | 2014-03-31 | | Release date: | 2014-06-04 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Structure, 26, 2018
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3BDP
 | | DNA POLYMERASE I/DNA COMPLEX | | Descriptor: | DNA (5'-D(*AP*GP*CP*AP*TP*CP*AP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*GP*CP*2DT)-3'), PROTEIN (DNA POLYMERASE I), ... | | Authors: | Kiefer, J.R, Mao, C, Beese, L.S. | | Deposit date: | 1997-11-17 | | Release date: | 1999-01-13 | | Last modified: | 2023-08-02 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.
Nature, 391, 1998
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2Z4S
 | | Crystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Chromosomal replication initiator protein dnaA, MAGNESIUM ION | | Authors: | Fujikawa, N, Ozaki, S, Kagawa, W, Park, S.-Y, Katayama, T, Kurumizaka, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-06-25 | | Release date: | 2008-02-19 | | Last modified: | 2024-08-14 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | A Common Mechanism for the ATP-DnaA-dependent Formation of Open Complexes at the Replication Origin.
J.Biol.Chem., 283, 2008
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3G9O
 | | GR DNA-binding domain:Sgk 16bp complex-9 | | Descriptor: | DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3'), Glucocorticoid receptor, ... | | Authors: | Pufall, M.A, Yamamoto, K.R, Meijsing, S.H. | | Deposit date: | 2009-02-13 | | Release date: | 2009-04-21 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | DNA binding site sequence directs glucocorticoid receptor structure and activity.
Science, 324, 2009
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6GN4
 | | tc-DNA/tc-DNA duplex | | Descriptor: | Tc-DNA (5'-D(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3'), Tc-DNA (5'-D(*(TCS)P*(TTK)P*(TCY)P*(TCY)P*(TCS)P*(TCJ)P*(TCJ)P*(TCS)P*(TCY)P*(TCS))-3') | | Authors: | Istrate, A, Johannsen, S, Istrate, A, Sigel, R.K.O, Leumann, C. | | Deposit date: | 2018-05-29 | | Release date: | 2018-06-06 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance.
Nucleic Acids Res., 47, 2019
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