1A36
 
 | | TOPOISOMERASE I/DNA COMPLEX | | Descriptor: | DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*A P*TP*TP*TP*TP*T)- 3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*C P*TP*TP*TP*TP*T)- 3'), TOPOISOMERASE I | | Authors: | Stewart, L, Redinbo, M.R, Qiu, X, Champoux, J.J, Hol, W.G.J. | | Deposit date: | 1998-01-29 | | Release date: | 1998-08-12 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | A model for the mechanism of human topoisomerase I.
Science, 279, 1998
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6CEV
 | | MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data | | Descriptor: | DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3'), Methyl-CpG-binding domain protein 3, ... | | Authors: | Liu, K, Tempel, W, Wernimont, A.K, Bountra, C, Arrowsmith, C.H, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC) | | Deposit date: | 2018-02-12 | | Release date: | 2018-05-09 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.005 Å) | | Cite: | Structural analyses reveal that MBD3 is a methylated CG binder.
Febs J., 286, 2019
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6CEU
 | | MBD3 MBD in complex with methylated, non-palindromic CpG DNA: alternative interpretation of crystallographic data | | Descriptor: | DNA (5'-D(*GP*CP*CP*AP*AP*(5CM)P*GP*CP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*GP*(5CM)P*GP*TP*TP*GP*GP*C)-3'), Methyl-CpG-binding domain protein 3, ... | | Authors: | Liu, K, Tempel, W, Wernimont, A.K, Bountra, C, Arrowsmith, C.H, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC) | | Deposit date: | 2018-02-12 | | Release date: | 2018-05-09 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.005 Å) | | Cite: | Structural analyses reveal that MBD3 is a methylated CG binder.
Febs J., 286, 2019
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8P5Q
 | | Structure of an ALOG domain from Arabidopsis thaliana in complex with DNA | | Descriptor: | DNA (5'-D(*AP*CP*GP*TP*CP*AP*AP*CP*AP*GP*TP*AP*AP*AP*CP*TP*A)-3'), DNA (5'-D(*TP*AP*GP*TP*TP*TP*AP*CP*TP*GP*TP*TP*GP*AP*CP*GP*T)-3'), Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3, ... | | Authors: | Zubieta, C, Nanao, M.H, Rieu, P. | | Deposit date: | 2023-05-24 | | Release date: | 2024-02-21 | | Last modified: | 2024-09-04 | | Method: | X-RAY DIFFRACTION (2.14 Å) | | Cite: | The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development.
Proc.Natl.Acad.Sci.USA, 121, 2024
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7Z9C
 | | E.coli gyrase holocomplex with 217 bp DNA and albicidin | | Descriptor: | DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3'), DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3'), DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3'), ... | | Authors: | Ghilarov, D, Heddle, J.G.H, Suessmuth, R. | | Deposit date: | 2022-03-21 | | Release date: | 2023-02-15 | | Last modified: | 2023-07-19 | | Method: | ELECTRON MICROSCOPY (3.06 Å) | | Cite: | Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.
Nat Catal, 6, 2023
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7LPH
 | | APE1 Mn-bound product complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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7LPG
 | | APE1 product complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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1LMB
 | | REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX | | Descriptor: | DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3'), DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3'), PROTEIN (LAMBDA REPRESSOR) | | Authors: | Beamer, L.J, Pabo, C.O. | | Deposit date: | 1991-11-05 | | Release date: | 1991-11-05 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Refined 1.8 A crystal structure of the lambda repressor-operator complex.
J.Mol.Biol., 227, 1992
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1PVQ
 | | BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7 | | Descriptor: | DNA 34-MER, Recombinase cre | | Authors: | Baldwin, E.P, Martin, S.S, Abel, J, Gelato, K.A, Kim, H, Schultz, P.G, Santoro, S.W. | | Deposit date: | 2003-06-28 | | Release date: | 2004-02-17 | | Last modified: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water.
Chem.Biol., 10, 2003
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8B8T
 | | Open conformation of the complex of DNA ligase I on PCNA and DNA in the presence of ATP | | Descriptor: | DNA ligase 1, Proliferating cell nuclear antigen | | Authors: | Blair, K, Tehseen, M, Raducanu, V.S, Shahid, T, Lancey, C, Cruehet, R, Hamdan, S, De Biasio, A. | | Deposit date: | 2022-10-05 | | Release date: | 2023-01-11 | | Last modified: | 2024-07-24 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing.
Nat Commun, 13, 2022
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5D4Z
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5D50
 | | Crystal structure of Rep-Ant complex from Salmonella-temperate phage | | Descriptor: | Anti-repressor protein, Repressor | | Authors: | Son, S.H, Yoon, H.J, Ryu, S, Lee, H.H. | | Deposit date: | 2015-08-10 | | Release date: | 2016-04-27 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor
Proc.Natl.Acad.Sci.USA, 113, 2016
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8F2W
 | | Structure of a B-Form Dodecamer: 5'-CGCGAATTCGCG-3 | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION | | Authors: | Ogbonna, E.N, Wilson, W.D. | | Deposit date: | 2022-11-08 | | Release date: | 2023-02-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Acs Bio Med Chem Au, 3, 2023
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7PLH
 | | Scytonema hofmannii TnsC bound to AMPPNP and DNA | | Descriptor: | DNA (5'-D(P*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'), MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Querques, I, Jinek, M. | | Deposit date: | 2021-08-31 | | Release date: | 2021-12-01 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (3.57 Å) | | Cite: | Target site selection and remodelling by type V CRISPR-transposon systems.
Nature, 599, 2021
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8F20
 | | Structure of an A-tract B-DNA Dodecamer: 5'-CGCAAAAAAGCG-3 | | Descriptor: | DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3') | | Authors: | Ogbonna, E.N, Wilson, W.D. | | Deposit date: | 2022-11-06 | | Release date: | 2023-02-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.23 Å) | | Cite: | X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Acs Bio Med Chem Au, 3, 2023
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7DKN
 | | Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase | | Descriptor: | Methylated-DNA--protein-cysteine methyltransferase, SULFATE ION | | Authors: | Kikuchi, M, Yamauchi, T, Iizuka, Y, Tsunoda, M. | | Deposit date: | 2020-11-25 | | Release date: | 2021-12-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase.
Acta Crystallogr.,Sect.F, 77, 2021
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7DQR
 | | Crystal structure of Sulfurisphaera tokodaii methylated O6-methylguanine methyltransferase | | Descriptor: | Methylated-DNA--protein-cysteine methyltransferase, SULFATE ION | | Authors: | Kikuchi, M, Yamauchi, T, Iizuka, Y, Tsonoda, M. | | Deposit date: | 2020-12-24 | | Release date: | 2021-12-15 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.74 Å) | | Cite: | Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase.
Acta Crystallogr.,Sect.F, 77, 2021
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7UIK
 | | Mediator-PIC Early (Tail A + Upstream DNA & Activator) | | Descriptor: | DNA (37-MER), DNA (38-MER), Mediator of RNA polymerase II transcription subunit 14, ... | | Authors: | Gorbea Colon, J.J, Chen, S.-F, Tsai, K.L, Murakami, K. | | Deposit date: | 2022-03-29 | | Release date: | 2023-03-01 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (7.7 Å) | | Cite: | Structural basis of a transcription pre-initiation complex on a divergent promoter.
Mol.Cell, 83, 2023
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6T78
 | | Structure of human Sox11 transcription factor in complex with a short DNA fragment | | Descriptor: | DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3'), DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3'), Transcription factor SOX-11 | | Authors: | Dodonova, S.O, Zhu, F, Dienemann, C, Taipale, J, Cramer, P. | | Deposit date: | 2019-10-21 | | Release date: | 2020-04-29 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.504 Å) | | Cite: | Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Nature, 580, 2020
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7LPJ
 | | APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase, ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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8GKH
 | | Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with omega RNA and target DNA | | Descriptor: | DNA (35-MER), DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3'), MAGNESIUM ION, ... | | Authors: | Xu, P, Saito, M, Zhang, F. | | Deposit date: | 2023-03-19 | | Release date: | 2023-07-05 | | Last modified: | 2023-08-30 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Fanzor is a eukaryotic programmable RNA-guided endonuclease.
Nature, 620, 2023
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7LPI
 | | APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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4WZW
 | | Crystal structure of human Puf-A in complex with DNA | | Descriptor: | DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'), DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3'), Pumilio domain-containing protein KIAA0020 | | Authors: | Qiu, C, Hall, T.M.T. | | Deposit date: | 2014-11-20 | | Release date: | 2014-12-31 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.9516 Å) | | Cite: | A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.
Proc.Natl.Acad.Sci.USA, 111, 2014
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8GN4
 | | The crystal structure of ZBTB10 ZF1-2 R767Q in complex with telomeric DNA TTAGGG | | Descriptor: | DNA (5'-D(*AP*TP*AP*TP*AP*AP*CP*CP*CP*TP*A)-3'), DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*TP*A)-3'), ZINC ION, ... | | Authors: | Li, F.D, Wang, S.M. | | Deposit date: | 2022-08-22 | | Release date: | 2023-08-30 | | Last modified: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-a-brac - zinc finger protein ZBTB10.
J.Biol.Chem., 299, 2023
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5KBJ
 | | Structure of Rep-DNA complex | | Descriptor: | DNA (32-MER), Replication initiator A, N-terminal | | Authors: | Schumacher, M. | | Deposit date: | 2016-06-03 | | Release date: | 2016-06-29 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3.09 Å) | | Cite: | Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein.
Proc. Natl. Acad. Sci. U.S.A., 111, 2014
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