PDB: 45817 resultsInfo pagesStatus searchChemie searchBIRD

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7C17	The cryo-EM structure of E. coli CueR transcription activation complex with fully duplex promoter DNA Descriptor: DNA (72-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Fang, C.L, Zhang, Y. Deposit date: 2020-05-02 Release date: 2020-09-30 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (4.22 Å) Cite: CueR activates transcription through a DNA distortion mechanism. Nat.Chem.Biol., 17, 2021
5FZ5	Transcription initiation complex structures elucidate DNA opening (CC) Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2, ... Authors: Plaschka, C, Hantsche, M, Dienemann, C, Burzinski, C, Plitzko, J, Cramer, P. Deposit date: 2016-03-10 Release date: 2016-05-18 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (8.8 Å) Cite: Transcription Initiation Complex Structures Elucidate DNA Opening Nature, 533, 2016
5FYW	Transcription initiation complex structures elucidate DNA opening (OC) Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2, ... Authors: Plaschka, C, Hantsche, M, Dienemann, C, Burzinski, C, Plitzko, J, Cramer, P. Deposit date: 2016-03-10 Release date: 2016-05-18 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (4.35 Å) Cite: Transcription Initiation Complex Structures Elucidate DNA Opening Nature, 533, 2016
5NSS	Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta',DNA-directed RNA polymerase subunit beta',DNA-directed RNA polymerase subunit beta', ... Authors: Glyde, R, Ye, F.Z, Darbari, V.C, Zhang, N, Buck, M, Zhang, X.D. Deposit date: 2017-04-26 Release date: 2017-06-28 Last modified: 2024-05-15 Method: ELECTRON MICROSCOPY (5.8 Å) Cite: Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol. Cell, 67, 2017
5NSR	Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Glyde, R, Ye, F.Z, Darbari, V.C, Zhang, N, Buck, M, Zhang, X.D. Deposit date: 2017-04-26 Release date: 2017-06-28 Last modified: 2019-12-11 Method: ELECTRON MICROSCOPY (3.8 Å) Cite: Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol. Cell, 67, 2017
8JH2	RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Descriptor: DNA (218-MER), DNA (40-MER), DNA-directed RNA polymerase subunit, ... Authors: Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. Deposit date: 2023-05-22 Release date: 2023-11-29 Last modified: 2023-12-20 Method: ELECTRON MICROSCOPY (5.7 Å) Cite: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem., 299, 2023
6LBW	Crystal structure of Ag-mediated base pairs in uncanonical DNA duplex Descriptor: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3'), SILVER ION Authors: Aoyama, H, Obika, S, Nakagawa, O. Deposit date: 2019-11-15 Release date: 2020-11-18 Last modified: 2024-03-27 Method: X-RAY DIFFRACTION (1.501 Å) Cite: Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry, 27, 2021
7QXI	Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... Authors: Ye, F.Z, Zhang, X.D. Deposit date: 2022-01-26 Release date: 2022-11-09 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (3.4 Å) Cite: Mechanisms of DNA opening revealed in AAA+ transcription complex structures. Sci Adv, 8, 2022
8H3V	Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC Descriptor: DNA (125-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Han, S.J, Jiang, Y.L, You, L.L, Shen, L.Q, Wu, X.X, Yang, F, Kong, W.W, Chen, Z.P, Zhang, Y, Zhou, C.Z. Deposit date: 2022-10-09 Release date: 2023-10-04 Last modified: 2024-02-28 Method: ELECTRON MICROSCOPY (4.5 Å) Cite: DNA looping mediates cooperative transcription activation. Nat.Struct.Mol.Biol., 31, 2024
8H40	Cryo-EM structure of the transcription activation complex NtcA-TAC Descriptor: DNA (125-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... Authors: Han, S.J, Jiang, Y.L, You, L.L, Shen, L.Q, Wu, X.X, Yang, F, Kong, W.W, Chen, Z.P, Zhang, Y, Zhou, C.Z. Deposit date: 2022-10-09 Release date: 2023-10-04 Last modified: 2024-02-28 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: DNA looping mediates cooperative transcription activation. Nat.Struct.Mol.Biol., 31, 2024
4WU4	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 22bp DNA Descriptor: DNA (5'-D(P*AP*AP*AP*TP*CP*GP*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3'), DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3'), GLYCEROL, ... Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-10-31 Release date: 2015-05-06 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.3 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
4WUL	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 26bp DNA Descriptor: DNA (26-MER), Response regulator receiver domain protein Authors: Davlieva, M, Shamoo, Y. Deposit date: 2014-11-02 Release date: 2015-05-06 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (2.4 Å) Cite: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
8JH4	RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Descriptor: DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... Authors: Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. Deposit date: 2023-05-22 Release date: 2023-11-29 Last modified: 2023-12-20 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem., 299, 2023
8JH3	RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Descriptor: DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... Authors: Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. Deposit date: 2023-05-22 Release date: 2023-11-29 Last modified: 2023-12-20 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J.Biol.Chem., 299, 2023
5TB9	Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)FTC-TP and Mn2+. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.49 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TBB	Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi. Descriptor: 10- MER PRIMER, 16- MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.39 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5TBA	Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC and PPi. Descriptor: 10-MER PRIMER, 16-MER TEMPLATE, 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER, ... Authors: Vyas, R, Suo, Z. Deposit date: 2016-09-11 Release date: 2017-01-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.49 Å) Cite: Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase. J. Am. Chem. Soc., 139, 2017
5T1J	Crystal Structure of the Tbox DNA binding domain of the transcription factor T-bet Descriptor: DNA, T-box transcription factor TBX21 Authors: Liu, C.F, Brandt, G.S, Hoang, Q, Hwang, E.S, Naumova, N, Lazarevic, V, Dekker, J, Glimcher, L.H, Ringe, D, Petsko, G.A. Deposit date: 2016-08-19 Release date: 2016-10-26 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.947 Å) Cite: Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. Proc.Natl.Acad.Sci.USA, 113, 2016
5T01	Human c-Jun DNA binding domain homodimer in complex with methylated DNA Descriptor: DNA (5'-D(*AP*AP*TP*GP*GP*AP*(5CM)P*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*G)-3'), DNA (5'-D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP*AP*T)-3'), Transcription factor AP-1 Authors: Hong, S, Horton, J.R, Cheng, X. Deposit date: 2016-08-15 Release date: 2017-03-01 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.89 Å) Cite: Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res., 45, 2017
5SWW	Crystal Structure of Human APOBEC3A complexed with ssDNA Descriptor: DNA 15-Mer, DNA dC->dU-editing enzyme APOBEC-3A, GLYCEROL, ... Authors: Shi, K, Banerjee, S, Kurahashi, K, Aihara, H. Deposit date: 2016-08-09 Release date: 2016-12-28 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (3.151 Å) Cite: Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol., 24, 2017
5T2W	Structure of thymine DNA glycosylase bound to substrate analog 2'-F-5-formyl-dC Descriptor: DNA (27-MER), DNA (28-MER), G/T mismatch-specific thymine DNA glycosylase Authors: Pidugu, L.S, Pozharski, E, Drohat, A.C. Deposit date: 2016-08-24 Release date: 2016-11-09 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase. Biochemistry, 55, 2016
5SZX	Epstein-Barr virus Zta DNA binding domain homodimer in complex with methylated DNA Descriptor: DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM)P*GP*AP*TP*GP*AP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM)P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3'), PHOSPHATE ION, ... Authors: Hong, S, Horton, J.R, Cheng, X. Deposit date: 2016-08-15 Release date: 2017-03-01 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.251 Å) Cite: Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res., 45, 2017
4TUP	Structure of human DNA polymerase beta complexed with GG as the template (GG0b) in a 1-nucleotide gapped DNA Descriptor: DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3'), DNA (5'-D(P*GP*TP*GP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2014-06-24 Release date: 2014-10-01 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.8 Å) Cite: Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta. J.Biol.Chem., 289, 2014
6XEO	Structure of Mfd bound to dsDNA Descriptor: DNA (5'-D(P*AP*GP*GP*AP*TP*AP*CP*TP*TP*AP*CP*AP*GP*CP*CP*AP*TP*C)-3'), DNA (5'-D(P*GP*AP*TP*GP*GP*CP*TP*GP*TP*AP*AP*GP*TP*AP*TP*CP*CP*T)-3'), Transcription-repair-coupling factor Authors: Brugger, C, Deaconescu, A. Deposit date: 2020-06-12 Release date: 2020-08-19 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (5.5 Å) Cite: Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Nat Commun, 11, 2020
5T0U	CTCF ZnF2-7 and DNA complex structure Descriptor: DNA (5'-D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*AP*GP*TP*GP*AP*GP*G)-3'), Transcriptional repressor CTCF, ... Authors: Hashimoto, H, Wang, D, Cheng, X. Deposit date: 2016-08-16 Release date: 2017-05-24 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (3.199 Å) Cite: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol. Cell, 66, 2017

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