6UPY
| RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E | Descriptor: | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, ... | Authors: | Oh, J, Wang, D. | Deposit date: | 2019-10-18 | Release date: | 2020-06-10 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (3.4 Å) | Cite: | RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA, 117, 2020
|
|
1L1M
| SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1 | Descriptor: | 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3', 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3', Lactose operon repressor | Authors: | Kalodimos, C.G, Bonvin, A.M.J.J, Salinas, R.K, Wechselberger, R, Boelens, R, Kaptein, R. | Deposit date: | 2002-02-19 | Release date: | 2002-06-26 | Last modified: | 2021-10-27 | Method: | SOLUTION NMR | Cite: | Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J., 21, 2002
|
|
7KC0
| Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp | Descriptor: | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (25-MER), DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3'), ... | Authors: | Zheng, F, Georgescu, R, Li, H, O'Donnell, M.E. | Deposit date: | 2020-10-04 | Release date: | 2020-12-02 | Last modified: | 2020-12-16 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA. Proc.Natl.Acad.Sci.USA, 117, 2020
|
|
2HT0
| IHF bound to doubly nicked DNA | Descriptor: | 5'-D(*CP*GP*GP*TP*GP*CP*AP*AP*CP*AP*AP*AP*T)-3', 5'-D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3', 5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)-3', ... | Authors: | Swinger, K.K, Rice, P.A. | Deposit date: | 2006-07-24 | Release date: | 2006-11-28 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure-based Analysis of HU-DNA Binding. J.Mol.Biol., 365, 2007
|
|
5YTY
| Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex | Descriptor: | 2-CARBOXYQUINOXALINE, DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3'), DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3'), ... | Authors: | Hou, M.H, Wu, P.C, Kao, Y.F. | Deposit date: | 2017-11-20 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex Nucleic Acids Res., 46, 2018
|
|
4UMM
| The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning | Descriptor: | 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE, 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP *AP*CP*TP*TP*GP*TP)-3', 5'-D(*DGP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*DAP *AP*CP*CP*CP*TP*T)-3', ... | Authors: | Maletta, M, Orlov, I, Moras, D, Billas, I.M.L, Klaholz, B.P. | Deposit date: | 2014-05-19 | Release date: | 2014-06-25 | Last modified: | 2024-05-08 | Method: | ELECTRON MICROSCOPY (11.6 Å) | Cite: | The Palindromic DNA-Bound Usp-Ecr Nuclear Receptor Adopts an Asymmetric Organization with Allosteric Domain Positioning. Nat.Commun., 5, 2014
|
|
5CIZ
| |
8KG8
| Yeast replisome in state II | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cell division control protein 45, DNA (61-mer), ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D, Xu, Z. | Deposit date: | 2023-08-17 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (4.23 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
|
|
8KG9
| Yeast replisome in state III | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cell division control protein 45, DNA (61-mer), ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D, Xu, Z. | Deposit date: | 2023-08-17 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (4.52 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
|
|
8KG6
| Yeast replisome in state I | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cell division control protein 45, Chromosome segregation in meiosis protein 3, ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D, Xu, Z. | Deposit date: | 2023-08-17 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (3.07 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
|
|
5YTZ
| Crystal structure of echinomycin-d(ACGTCGT)2 complex | Descriptor: | 2-CARBOXYQUINOXALINE, DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3'), Echinomycin, ... | Authors: | Hou, M.H, Wu, P.C, Kao, Y.F. | Deposit date: | 2017-11-20 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex Nucleic Acids Res., 46, 2018
|
|
6BLP
| Pol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP | Descriptor: | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, ... | Authors: | Wang, W, Wang, D. | Deposit date: | 2017-11-11 | Release date: | 2018-02-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.203 Å) | Cite: | Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
|
|
4RZR
| Bypass of a bulky adduct dG1,8 by DPO4 | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CALCIUM ION, ... | Authors: | Vyas, R, Suo, Z. | Deposit date: | 2014-12-23 | Release date: | 2015-09-16 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase. J.Am.Chem.Soc., 137, 2015
|
|
6BM4
| Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP | Descriptor: | 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine, DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), DNA-directed RNA polymerase II subunit RPB1, ... | Authors: | Wang, W, Wang, D. | Deposit date: | 2017-11-13 | Release date: | 2018-02-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.951 Å) | Cite: | Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A., 115, 2018
|
|
5K1Y
| |
8W7M
| Yeast replisome in state V | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Cell division control protein 45, DNA (71-mer), ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D, Xu, Z. | Deposit date: | 2023-08-30 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (4.12 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
|
|
8W7S
| Yeast replisome in state IV | Descriptor: | Cell division control protein 45, DNA (71-mer), DNA polymerase alpha-binding protein, ... | Authors: | Dang, S, Zhai, Y, Feng, J, Yu, D. | Deposit date: | 2023-08-31 | Release date: | 2023-12-20 | Method: | ELECTRON MICROSCOPY (7.39 Å) | Cite: | Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun, 14, 2023
|
|
4MNB
| Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA | Descriptor: | 5'-D(*CP*GP*TP*AP*CP*G)-3', 9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol, COBALT (II) ION, ... | Authors: | Canals, A, Arribas-Bosacoma, R, Alvarez, M, Albericio, F, Aymami, J, Coll, M. | Deposit date: | 2013-09-10 | Release date: | 2015-03-11 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Intercalative DNA binding of the marine anticancer drug variolin B. Sci Rep, 7, 2017
|
|
5YZE
| Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex | Descriptor: | (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose, 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate, 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol, ... | Authors: | Hou, M.H, Chen, Y.W, Wu, P.C, Satange, R.B. | Deposit date: | 2017-12-14 | Release date: | 2018-10-17 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.87 Å) | Cite: | CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex Int J Mol Sci, 19, 2018
|
|
7QWV
| Crystal structure of the REC114-TOPOVIBL complex. | Descriptor: | Meiotic recombination protein REC114, Type 2 DNA topoisomerase 6 subunit B-like | Authors: | Juarez-Martinez, A.B, Robert, T, de Massy, B, Kadlec, J. | Deposit date: | 2022-01-25 | Release date: | 2023-02-01 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.26 Å) | Cite: | TOPOVIBL-REC114 interaction regulates meiotic DNA double-strand breaks. Nat Commun, 13, 2022
|
|
4QWQ
| Crystal structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus | Descriptor: | Response regulator SaeR | Authors: | Fan, X, Zhu, Y, Zhang, X, Teng, M, Li, X. | Deposit date: | 2014-07-17 | Release date: | 2015-08-19 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.501 Å) | Cite: | Structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus. Acta Crystallogr.,Sect.D, 71, 2015
|
|
4MZ9
| Revised structure of E. coli SSB | Descriptor: | Single-stranded DNA-binding protein | Authors: | Oakley, A.J. | Deposit date: | 2013-09-29 | Release date: | 2013-12-18 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy. Nucleic Acids Res., 42, 2014
|
|
6TW3
| HumRadA2 in complex with Naphthyl-HPA fragment-peptide chimera | Descriptor: | (2~{S})-1-[(2~{S})-2-[(3-azanylnaphthalen-2-yl)carbonylamino]-3-(1~{H}-imidazol-4-yl)propanoyl]-~{N}-[(2~{S})-1-azanyl-1-oxidanylidene-propan-2-yl]pyrrolidine-2-carboxamide, DNA repair and recombination protein RadA, PHOSPHATE ION | Authors: | Marsh, M.E, Fischer, G, Scott, D.E, Coyne, A.G, Skidmore, J, Abell, C, Hyvonen, M. | Deposit date: | 2020-01-12 | Release date: | 2021-01-27 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.352 Å) | Cite: | A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol, 28, 2021
|
|
6TW4
| HumRadA22F in complex with compound 6 | Descriptor: | CALCIUM ION, DNA repair and recombination protein RadA, ~{N}-[2-[(2~{S})-2-[[(1~{S})-1-(4-methoxyphenyl)ethyl]carbamoyl]pyrrolidin-1-yl]-2-oxidanylidene-ethyl]quinoline-2-carboxamide | Authors: | Marsh, M.E, Scott, D.E, Coyne, A.G, Skidmore, J, Abell, C, Hyvonen, M. | Deposit date: | 2020-01-12 | Release date: | 2021-01-27 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.73 Å) | Cite: | A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol, 28, 2021
|
|
6TW9
| HumRadA22F in complex with CAM833 | Descriptor: | CALCIUM ION, DNA repair and recombination protein RadA, GLYCEROL, ... | Authors: | Fischer, G, Marsh, M.E, Scott, D.E, Coyne, A.G, Skidmore, J, Abell, C, Hyvonen, M. | Deposit date: | 2020-01-12 | Release date: | 2021-01-27 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.52 Å) | Cite: | A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death. Cell Chem Biol, 28, 2021
|
|