PDB: 2866 resultsInfo pagesStatus searchChemie searchBIRD

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7LFQ	Pyrococcus RNA ligase Descriptor: DNA (5'-D(*AP*TP*GP*TP*CP*C)-3'), POTASSIUM ION, RNA-splicing ligase RtcB, ... Authors: Goldgur, Y, Shuman, S, Banerjee, A. Deposit date: 2021-01-18 Release date: 2021-03-03 Last modified: 2023-11-15 Method: X-RAY DIFFRACTION (2.7 Å) Cite: Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide. Rna, 27, 2021
4RKG	Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA Descriptor: DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3'), E3 ubiquitin-protein ligase msl-2, ZINC ION Authors: Zheng, S, Ye, K. Deposit date: 2014-10-13 Release date: 2015-01-21 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation. Genes Dev., 28, 2014
6R8Z	Cryo-EM structure of NCP_THF2(-1)-UV-DDB Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ... Authors: Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H. Deposit date: 2019-04-02 Release date: 2019-06-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (3.9 Å) Cite: DNA damage detection in nucleosomes involves DNA register shifting. Nature, 571, 2019
6R90	Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ... Authors: Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H. Deposit date: 2019-04-02 Release date: 2019-06-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4.5 Å) Cite: DNA damage detection in nucleosomes involves DNA register shifting. Nature, 571, 2019
6R8Y	Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ... Authors: Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H. Deposit date: 2019-04-02 Release date: 2019-06-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4.3 Å) Cite: DNA damage detection in nucleosomes involves DNA register shifting. Nature, 571, 2019
6R91	Cryo-EM structure of NCP_THF2(-3)-UV-DDB Descriptor: DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ... Authors: Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H. Deposit date: 2019-04-02 Release date: 2019-06-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4.1 Å) Cite: DNA damage detection in nucleosomes involves DNA register shifting. Nature, 571, 2019
2ZKD	Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA Descriptor: 1,2-ETHANEDIOL, ACETATE ION, DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3'), ... Authors: Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M. Deposit date: 2008-03-19 Release date: 2008-09-09 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (1.6 Å) Cite: Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism Nature, 455, 2008
6M2V	Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. Descriptor: DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3'), E3 ubiquitin-protein ligase UHRF1 Authors: Abhishek, S, Nakarakanti, N.K, Deeksha, W, Rajakumara, E. Deposit date: 2020-03-01 Release date: 2021-01-13 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (3 Å) Cite: Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int.J.Biol.Macromol., 170, 2021
6R92	Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Descriptor: DNA damage-binding protein 1,DNA damage-binding protein 1, DNA damage-binding protein 2, Histone H2A type 1-B/E, ... Authors: Matsumoto, S, Cavadini, S, Bunker, R.D, Thoma, N.H. Deposit date: 2019-04-02 Release date: 2019-06-12 Last modified: 2024-05-22 Method: ELECTRON MICROSCOPY (4.8 Å) Cite: DNA damage detection in nucleosomes involves DNA register shifting. Nature, 571, 2019
5CKK	Crystal structure of 9DB1* deoxyribozyme Descriptor: DNA (44-MER), MAGNESIUM ION, RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)-3') Authors: Ponce-Salvatierra, A, Hoebartner, C, Pena, V. Deposit date: 2015-07-15 Release date: 2016-01-13 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (2.801 Å) Cite: Crystal structure of a DNA catalyst. Nature, 529, 2016
7K01	Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Descriptor: DNA repair helicase RAD25, DNA repair helicase RAD3, General transcription and DNA repair factor IIH subunit SSL1, ... Authors: van Eeuwen, T, Min, J.H, Murakami, K. Deposit date: 2020-09-02 Release date: 2021-07-28 Method: ELECTRON MICROSCOPY (3.9 Å) Cite: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. Nat Commun, 12, 2021
8EWV	DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Descriptor: Bromodomain-containing protein 4, Elongin-B, Elongin-C, ... Authors: Schreiber, S.L, Shu, W, Ma, X, Michaud, G, Bonazzi, S, Berst, F. Deposit date: 2022-10-24 Release date: 2023-10-04 Last modified: 2024-02-14 Method: X-RAY DIFFRACTION (3.4 Å) Cite: DNA-encoded library-enabled discovery of proximity-inducing small molecules. Nat.Chem.Biol., 20, 2024
4CI3	Structure of the DDB1-CRBN E3 ubiquitin ligase bound to Pomalidomide Descriptor: DNA DAMAGE-BINDING PROTEIN 1, PROTEIN CEREBLON, S-Pomalidomide, ... Authors: Fischer, E.S, Boehm, K, Thoma, N.H. Deposit date: 2013-12-05 Release date: 2014-07-16 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (3.5 Å) Cite: Structure of the Ddb1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide. Nature, 512, 2014
4CI2	Structure of the DDB1-CRBN E3 ubiquitin ligase bound to lenalidomide Descriptor: DNA DAMAGE-BINDING PROTEIN 1, PROTEIN CEREBLON, S-Lenalidomide, ... Authors: Fischer, E.S, Boehm, K, Thoma, N.H. Deposit date: 2013-12-05 Release date: 2014-07-16 Last modified: 2024-05-01 Method: X-RAY DIFFRACTION (2.95 Å) Cite: Structure of the Ddb1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide. Nature, 512, 2014
3RCZ	Rad60 SLD2 Ubc9 Complex Descriptor: DNA repair protein rad60, SUMO-conjugating enzyme ubc9 Authors: Perry, J.J.P, Arvai, A.S, Tainer, J.A. Deposit date: 2011-03-31 Release date: 2011-04-27 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (1.9 Å) Cite: DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes. Mol.Cell.Biol., 31, 2011
6Q00	TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1 Descriptor: POTASSIUM ION, Tyrosyl-DNA phosphodiesterase 2, Ubiquitin Authors: Schellenberg, M.J, Krahn, J.M, Williams, R.S. Deposit date: 2019-08-01 Release date: 2020-04-29 Last modified: 2020-06-24 Method: X-RAY DIFFRACTION (0.85 Å) Cite: Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2. Nucleic Acids Res., 48, 2020
6WGC	Atomic model of semi-attached mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) Descriptor: Cell division control protein 6, DNA (41-MER), DNA replication licensing factor MCM3, ... Authors: Yuan, Z, Schneider, S, Dodd, T, Riera, A, Bai, L, Yan, C, Magdalou, I, Ivanov, I, Stillman, B, Li, H, Speck, C. Deposit date: 2020-04-05 Release date: 2020-07-15 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (4.3 Å) Cite: Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proc.Natl.Acad.Sci.USA, 117, 2020
3SR2	Crystal Structure of Human XLF-XRCC4 Complex Descriptor: DNA repair protein XRCC4, Non-homologous end-joining factor 1 Authors: Hammel, M, Classen, S, Tainer, J.A. Deposit date: 2011-07-06 Release date: 2011-07-20 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (3.9708 Å) Cite: XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair. J.Biol.Chem., 286, 2011
6WGG	Atomic model of pre-insertion mutant OCCM-DNA complex(ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) Descriptor: Cell division control protein 6, Cell division cycle protein CDT1, DNA (41-MER), ... Authors: Yuan, Z, Schneider, S, Dodd, T, Riera, A, Bai, L, Yan, C, Magdalou, I, Ivanov, I, Stillman, B, Li, H, Speck, C. Deposit date: 2020-04-05 Release date: 2020-07-15 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (8.1 Å) Cite: Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proc.Natl.Acad.Sci.USA, 117, 2020
6WGI	Atomic model of the mutant OCCM (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) loaded on DNA at 10.5 A resolution Descriptor: Cell division control protein 6, Cell division cycle protein CDT1, DNA (34-MER), ... Authors: Yuan, Z, Schneider, S, Dodd, T, Riera, A, Bai, L, Yan, C, Magdalou, I, Ivanov, I, Stillman, B, Li, H, Speck, C. Deposit date: 2020-04-05 Release date: 2020-07-15 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (10 Å) Cite: Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proc.Natl.Acad.Sci.USA, 117, 2020
6OEM	Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) Descriptor: DNA (46-MER), DNA (57-MER), High mobility group protein B1, ... Authors: Chen, X, Cui, Y, Zhou, Z.H, Yang, W, Gellert, M. Deposit date: 2019-03-27 Release date: 2020-01-29 Last modified: 2024-11-06 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Cutting antiparallel DNA strands in a single active site. Nat.Struct.Mol.Biol., 27, 2020
5NP7	CryoEM structure of Human Rad51 on single-stranded DNA to 4.2A resolution. Descriptor: DNA repair protein RAD51 homolog 1, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Authors: Short, J.M, Venkitaraman, A. Deposit date: 2017-04-13 Release date: 2017-05-03 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (4.2 Å) Cite: High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Res., 44, 2016
2D8M	Solution structure of the first BRCT domain of DNA-repair protein XRCC1 Descriptor: DNA-repair protein XRCC1 Authors: Nagashima, T, Hayashi, F, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2005-12-06 Release date: 2006-06-06 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Solution structure of the first BRCT domain of DNA-repair protein XRCC1 To be published
3SZQ	Structure of an S. pombe APTX/DNA/AMP/Zn complex Descriptor: 5'-D(*CP*CP*CP*TP*G)-3', 5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3', ADENOSINE MONOPHOSPHATE, ... Authors: Tumbale, P, Krahn, J, Williams, R.S. Deposit date: 2011-07-19 Release date: 2011-10-12 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (2.353 Å) Cite: Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease. Nat.Struct.Mol.Biol., 18, 2011
3Q4F	Crystal structure of xrcc4/xlf-cernunnos complex Descriptor: DNA repair protein XRCC4, Non-homologous end-joining factor 1 Authors: Ropars, V, Legrand, P, Charbonnier, J.B. Deposit date: 2010-12-23 Release date: 2011-08-03 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (5.5 Å) Cite: Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining. Proc.Natl.Acad.Sci.USA, 108, 2011

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