PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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7UOG	Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and asymmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence. Descriptor: DNA (5'-D(AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*CP*CP*GP*CP*CP*TP*T)-3', DNA (5'-D(GP*TP*AP*AP*GP*GP*CP*GP*GP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)-3', MAGNESIUM ION, ... Authors: Ward, A.R, Snow, C.D. Deposit date: 2022-04-12 Release date: 2023-04-19 Last modified: 2023-11-01 Method: X-RAY DIFFRACTION (2.63 Å) Cite: Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds. Acs Nano, 17, 2023
9CEX	Spizellomyces punctatus Fanzor (SpuFz) State 4 Descriptor: DNA (29-MER), DNA (5'-D(*(MG)*(MG)P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'), DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3'), ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.27 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CA0	Human TOP3B-TDRD3 core complex in DNA pre-cleavage state Descriptor: DNA (5'-D(*AP*TP*T)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3'), DNA topoisomerase 3-beta-1, ... Authors: Yang, X, Chen, X, Yang, W, Pommier, Y. Deposit date: 2024-06-16 Release date: 2024-07-17 Last modified: 2024-10-30 Method: ELECTRON MICROSCOPY (3.48 Å) Cite: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics To Be Published
9BAQ	CryoEM structure of DIM2-HP1-H3K9me3-DNA complex Descriptor: DNA (5'-D(*AP*CP*TP*AP*CP*T)-R(P*(PYO))-D(P*CP*TP*CP*CP*TP*CP*CP*TP*AP*CP*T)-3'), DNA (5'-D(*AP*GP*TP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*TP*AP*GP*T)-3'), DNA (cytosine-5-)-methyltransferase, ... Authors: Song, J, Shao, Z. Deposit date: 2024-04-04 Release date: 2024-07-24 Method: ELECTRON MICROSCOPY (2.79 Å) Cite: CryoEM structure of DIM2-HP1-H3K9me3-DNA complex To Be Published
9CEW	Spizellomyces punctatus Fanzor (SpuFz) State 3 Descriptor: DNA (29-MER), DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'), DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3'), ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (2.88 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
5E17	T. thermophilus transcription initiation complex having a RRR discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 7 (RPo-GGG-7) Descriptor: DNA (27-MER), DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Zhang, Y, Ebright, R.H. Deposit date: 2015-09-29 Release date: 2016-03-09 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science, 351, 2016
5E18	T. thermophilus transcription initiation complex having a YYY discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 8 (RPo-CCC-8) Descriptor: DNA (28-MER), DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'), DNA-directed RNA polymerase subunit alpha, ... Authors: Zhang, Y, Ebright, R.H. Deposit date: 2015-09-29 Release date: 2016-03-09 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.3 Å) Cite: Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science, 351, 2016
9CA1	Human TOP3B-TDRD3 core complex in DNA religation state Descriptor: DNA (5'-D(*AP*TP*T)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3'), DNA topoisomerase 3-beta-1, ... Authors: Yang, X, Chen, X, Yang, W, Pommier, Y. Deposit date: 2024-06-16 Release date: 2024-07-17 Last modified: 2024-10-30 Method: ELECTRON MICROSCOPY (3.26 Å) Cite: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics To Be Published
9CF2	Parasitella parasitica Fanzor (PpFz) State 3 Descriptor: DNA non-target strand, DNA substrate model, DNA target strand, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.15 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9DP3	APE1 N174D Product Complex with Abasic 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*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... Authors: Hoitsma, N.M, DeHart, K.D, Freudenthal, B.D. Deposit date: 2024-09-20 Release date: 2024-10-09 Method: X-RAY DIFFRACTION (2.1 Å) Cite: N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction To Be Published
2DUN	Solution structure of BRCT domain of DNA polymerase mu Descriptor: DNA polymerase mu Authors: Nagashima, T, Hayashi, F, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposit date: 2006-07-25 Release date: 2007-01-25 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Solution structure of BRCT domain of DNA polymerase mu To be Published
9BW1	TnsABCD-DNA transpososome Descriptor: ADENOSINE-5'-TRIPHOSPHATE, Integrase, LE_polyA, ... Authors: Chang, L, Wang, S. Deposit date: 2024-05-20 Release date: 2024-10-16 Method: ELECTRON MICROSCOPY (3.65 Å) Cite: Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition. Cell, 2024
9CES	Guillardia theta Fanzor (GtFz) State 2 Descriptor: DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*TP*AP*AP*AP*GP*GP*CP*CP*CP*CP*GP*GP*G)-3'), DNA (5'-D(P*CP*CP*CP*GP*GP*GP*GP*CP*CP*TP*TP*TP*AP*AP*G)-3'), Maltose/maltodextrin-binding periplasmic protein,Guillardia theta Fanzor1, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-09 Method: ELECTRON MICROSCOPY (3.28 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
5XJ0	T. thermophilus RNA polymerase holoenzyme bound with gp39 and gp76 Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Ooi, W.Y, Murayama, Y, Mekler, V, Minakhin, L, Severinov, K, Yokoyama, S, Sekine, S. Deposit date: 2017-04-28 Release date: 2017-12-20 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (4.004 Å) Cite: A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation Nucleic Acids Res., 46, 2018
9C9Y	Human TOP3B-TDRD3 core complex in DNA pre-cleavage state Descriptor: DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*T)-3'), DNA topoisomerase 3-beta-1, MANGANESE (II) ION, ... Authors: Yang, X, Chen, X, Yang, W, Pommier, Y. Deposit date: 2024-06-16 Release date: 2024-07-17 Method: ELECTRON MICROSCOPY (3.35 Å) Cite: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics To Be Published
9CF1	Parasitella parasitica Fanzor (PpFz) State 2 Descriptor: DNA non-target strand, DNA target strand, Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.52 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CF3	Parasitella parasitica Fanzor (PpFz) State 4 Descriptor: DNA non-target strand, DNA target strand, MAGNESIUM ION, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9GSQ	DNA binding domain of J-DNA Binding Protein 3 (JBP3) Descriptor: CHLORIDE ION, DNA binding domain of J-DNA binding protein 3, GLYCEROL, ... Authors: de Vries, I, Adamopoulos, A, Joosten, R.P, Perrakis, A. Deposit date: 2024-09-16 Release date: 2024-09-25 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Base-J binding proteins JBP1 and JBP3 have conserved structures of their J-DNA binding domain but drastically different affinities To Be Published
9CF0	Parasitella parasitica Fanzor (PpFz) State 1 Descriptor: DNA non-target strand, DNA target strand, Maltose/maltodextrin-binding periplasmic protein,Parasitella parasitica Fanzor 1, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.47 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CEV	Spizellomyces punctatus Fanzor (SpuFz) State 2 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: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.26 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CEY	Spizellomyces punctatus Fanzor (SpuFz) State 5 Descriptor: DNA (26-MER), DNA (36-MER), MAGNESIUM ION, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.22 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CEZ	Spizellomyces punctatus Fanzor (SpuFz) State 6 Descriptor: DNA (27-MER), DNA (5'-D(P*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3'), MAGNESIUM ION, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.41 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CEU	Spizellomyces punctatus Fanzor (SpuFz) State 1 Descriptor: DNA (5'-D(P*CP*CP*TP*AP*TP*AP*GP*AP*TP*AP*TP*GP*CP*CP*CP*GP*GP*GP*TP*AP*CP*CP*G)-3'), DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3'), Maltose/maltodextrin-binding periplasmic protein,Spizellomyces punctatus Fanzor 1, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-02 Method: ELECTRON MICROSCOPY (3.29 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
9CET	Guillardia theta Fanzor (GtFz) State 3 Descriptor: DNA (28-MER), DNA (5'-D(P*AP*TP*GP*AP*CP*TP*TP*CP*TP*CP*TP*TP*AP*AP*AP*GP*GP*CP*CP*CP*CP*GP*GP*G)-3'), Maltose/maltodextrin-binding periplasmic protein,Guillardia theta Fanzor1, ... Authors: Xu, P, Saito, M, Zhang, F. Deposit date: 2024-06-27 Release date: 2024-09-11 Last modified: 2024-10-16 Method: ELECTRON MICROSCOPY (3 Å) Cite: Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell, 187, 2024
1O3Q	PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES Descriptor: 5'-D(*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3', 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*T)-3', ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, ... Authors: Chen, S, Vojtechovsky, J, Parkinson, G.N, Ebright, R.H, Berman, H.M. Deposit date: 2003-03-18 Release date: 2003-04-08 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (3 Å) Cite: Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking J.Mol.Biol., 314, 2001

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