PDB: 49006 resultsInfo pagesStatus searchChemie searchBIRD

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6EN1	Structure of the Tn1549 transposon Integrase (aa 82-397, R225K) in complex with a circular intermediate DNA (CI6a-DNA) Descriptor: DI(HYDROXYETHYL)ETHER, DNA (45-MER), Int protein Authors: Rubio-Cosials, A, Barabas, O. Deposit date: 2017-10-04 Release date: 2018-04-04 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (2.67 Å) Cite: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell, 173, 2018
6L5A	The structure of the UdgX mutant H109E at a pre-excision state Descriptor: GLYCEROL, IRON/SULFUR CLUSTER, Uracil DNA glycosylase superfamily protein Authors: Xie, W, Tu, J, Zeng, H. Deposit date: 2019-10-22 Release date: 2020-10-28 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (1.80007327 Å) Cite: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability. DNA Repair (Amst), 97, 2021
5CPK	Nucleosome containing methylated Sat2L DNA Descriptor: DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... Authors: Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H. Deposit date: 2015-07-21 Release date: 2015-10-28 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.632 Å) Cite: Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5, 2015
5CPI	Nucleosome containing unmethylated Sat2R DNA Descriptor: DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... Authors: Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H. Deposit date: 2015-07-21 Release date: 2015-10-28 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.902 Å) Cite: Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5, 2015
7WAY	PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state Descriptor: DNA (27-MER), DNA (33-MER), RNA, ... Authors: Zhang, S, Liu, J.J.G. Deposit date: 2021-12-15 Release date: 2022-03-16 Last modified: 2025-07-02 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol.Cell, 82, 2022
7WB1	PlmCasX-sgRNAv2-dsDNA ternary complex at nts loading state Descriptor: NTS-DNA, RNA (121-MER), TS-DNA, ... Authors: Zhang, S, Liu, J.J.G. Deposit date: 2021-12-15 Release date: 2022-03-16 Last modified: 2025-06-25 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol.Cell, 82, 2022
5GHT	DNA replication protein Descriptor: SsDNA-specific exonuclease Authors: Oyama, T. Deposit date: 2016-06-20 Release date: 2016-10-12 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.795 Å) Cite: Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. Nucleic Acids Res., 44, 2016
5Z7D	p204HINab-dsDNA complex structure Descriptor: DNA (5'-D(P*CP*CP*AP*TP*CP*AP*GP*AP*AP*AP*GP*AP*GP*AP*GP*C)-3'), Interferon-activable protein 204 Authors: Jin, T, Jiang, J, Xiao, T.S. Deposit date: 2018-01-28 Release date: 2019-01-30 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (4.5 Å) Cite: Structural mechanism of DNA recognition by the p204 HIN domain. Nucleic Acids Res., 2021
6MC2	Crystal structure of a tetrameric DNA fold-back quadruplex Descriptor: DNA (5'-D(*CP*GP*TP*AP*AP*GP*GP*CP*G)-3'), MAGNESIUM ION Authors: Chu, B, Paukstelis, P.J. Deposit date: 2018-08-30 Release date: 2018-11-14 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.05 Å) Cite: Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex. J. Am. Chem. Soc., 140, 2018
3SQ5	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant Descriptor: Tyrosyl-DNA phosphodiesterase 1 Authors: Gajewski, S, White, S.W. Deposit date: 2011-07-04 Release date: 2011-12-28 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J.Mol.Biol., 415, 2012
3SQ8	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase 1 H432R Mutant (SCAN1 Mutant) Descriptor: Tyrosyl-DNA phosphodiesterase 1 Authors: Gajewski, S, White, S.W. Deposit date: 2011-07-05 Release date: 2011-12-28 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J.Mol.Biol., 415, 2012
3SQ3	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H182A Mutant Descriptor: Tyrosyl-DNA phosphodiesterase 1 Authors: Gajewski, S, White, S.W. Deposit date: 2011-07-04 Release date: 2011-12-28 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J.Mol.Biol., 415, 2012
5W7O	2-Se-T4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Descriptor: DNA (5'-D(*AP*TP*GP*(US3)P*CP*G)-3'), MAGNESIUM ION, RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'), ... Authors: Fang, Z, Yang, F, Huang, Z. Deposit date: 2017-06-20 Release date: 2017-06-28 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.75 Å) Cite: 2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant To Be Published
5YX2	Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites Descriptor: DNA (25-MER), DNA (cytosine-5)-methyltransferase 3-like, DNA (cytosine-5)-methyltransferase 3A, ... Authors: Zhang, Z.M, Song, J. Deposit date: 2017-12-01 Release date: 2018-01-31 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.653 Å) Cite: Structural basis for DNMT3A-mediated de novo DNA methylation. Nature, 554, 2018
479D	CRYSTAL STRUCTURE A DNA:RNA HYBRID DUPLEX, A DYNAMIC MODEL FOR RNASE H RECOGNITION Descriptor: DNA (5'-D(*CP*TP*CP*TP*TP*CP*TP*TP*C)-3'), RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') Authors: Xiong, Y, Sundaralingam, M. Deposit date: 1999-07-08 Release date: 2000-05-15 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (1.9 Å) Cite: Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucleic Acids Res., 28, 2000
3UGM	Structure of TAL effector PthXo1 bound to its DNA target Descriptor: DNA-1, DNA-2, TAL effector AvrBs3/PthA Authors: Mak, A.N.S, Bradley, P, Cernadas, R.A, Bogdanove, A.J, Stoddard, B.L. Deposit date: 2011-11-02 Release date: 2012-01-04 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (3 Å) Cite: The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target. Science, 335, 2012
5US2	2-Se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Descriptor: DNA (5'-D(*AP*(US3)P*GP*TP*CP*G)-3'), MAGNESIUM ION, RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'), ... Authors: Fang, Z, Yang, F, Huang, Z. Deposit date: 2017-02-13 Release date: 2017-03-08 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.9 Å) Cite: 2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant To Be Published
6BRR	Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites Descriptor: DNA (25-MER), DNA (cytosine-5)-methyltransferase 3-like, DNA (cytosine-5)-methyltransferase 3A, ... Authors: Zhang, Z.M, Song, J. Deposit date: 2017-11-30 Release date: 2018-01-31 Last modified: 2024-12-25 Method: X-RAY DIFFRACTION (2.97 Å) Cite: Structural basis for DNMT3A-mediated de novo DNA methylation. Nature, 554, 2018
4C2T	Crystal structure of full length Deinococcus radiodurans UvrD in complex with DNA Descriptor: DNA HELICASE II, DNA STRAND FOR28, DNA STRAND REV28, ... Authors: Stelter, M, Acajjaoui, S, McSweeney, S, Timmins, J. Deposit date: 2013-08-20 Release date: 2013-10-30 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (3.997 Å) Cite: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Plos One, 8, 2013
4C30	Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2 Descriptor: DNA HELICASE II, DNA STRAND FOR25, DNA STRAND REV25, ... Authors: Stelter, M, Acajjaoui, S, McSweeney, S, Timmins, J. Deposit date: 2013-08-21 Release date: 2013-10-30 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Plos One, 8, 2013
4KPY	DNA binding protein and DNA complex structure Descriptor: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'), DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), ... Authors: Sheng, G, Zhao, H, Wang, J, Rao, Y, Wang, Y. Deposit date: 2013-05-14 Release date: 2014-01-29 Last modified: 2024-05-29 Method: X-RAY DIFFRACTION (2.406 Å) Cite: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc.Natl.Acad.Sci.USA, 111, 2014
5BT2	MeCP2 MBD domain (A140V) in complex with methylated DNA Descriptor: DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3'), Methyl-CpG-binding protein 2 Authors: Ho, K.L, Chia, J.Y, Tan, W.S, Ng, C.L, Hu, N.J, Foo, H.L. Deposit date: 2015-06-02 Release date: 2016-08-17 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.2 Å) Cite: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence. Sci Rep, 6, 2016
4ED6	Human DNA polymerase eta - DNA ternary complex: Reaction in the AT crystal at pH 6.7 for 15 hr, Sideway translocation Descriptor: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3'), DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Nakamura, T, Zhao, Y, Yang, W. Deposit date: 2012-03-27 Release date: 2012-07-11 Last modified: 2024-03-20 Method: X-RAY DIFFRACTION (2.211 Å) Cite: Watching DNA polymerase eta make a phosphodiester bond Nature, 487, 2012
6DBX	Cryo-EM structure of RAG in complex with 12-RSS substrate DNA Descriptor: CALCIUM ION, Forward strand of 12-RSS substrate DNA, Recombination activating gene 1 - MBP chimera, ... Authors: Wu, H, Liao, M, Ru, H, Mi, W. Deposit date: 2018-05-03 Release date: 2018-08-01 Last modified: 2024-03-13 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: DNA melting initiates the RAG catalytic pathway. Nat. Struct. Mol. Biol., 25, 2018
6IUE	DNA helical wire containing Hg(II) Descriptor: DNA (5'-D(*TP*TP*TP*GP*C)-3'), MERCURY (II) ION Authors: Ono, A, Kanazawa, H, Ito, H, Goto, M, Nakamura, K, Saneyoshi, H, Kondo, J. Deposit date: 2018-11-28 Release date: 2019-10-16 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (1.901 Å) Cite: A Novel DNA Helical Wire Containing HgII-Mediated T:T and T:G Pairs. Angew.Chem.Int.Ed.Engl., 58, 2019

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