5ZRF
 
 | | Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21 | | Descriptor: | (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside, DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3'), DNA topoisomerase 2-beta, ... | | Authors: | Chen, S.F, Wang, Y.R, Wu, C.C, Chan, N.L. | | Deposit date: | 2018-04-24 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.
Nat Commun, 9, 2018
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6A5T
 | | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | | Deposit date: | 2018-06-25 | | Release date: | 2018-10-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (6.7 Å) | | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
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6IR9
 | | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2018-11-12 | | Release date: | 2019-02-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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6A5U
 | | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation | | Descriptor: | DNA (198-MER), DNA (40-MER), DNA-directed RNA polymerase subunit, ... | | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | | Deposit date: | 2018-06-25 | | Release date: | 2018-10-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (7.6 Å) | | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
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6A5P
 | | RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | | Deposit date: | 2018-06-25 | | Release date: | 2018-10-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (7 Å) | | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
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6INQ
 | | RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) | | Descriptor: | DNA (198-MER), DNA (31-MER), DNA-directed RNA polymerase subunit, ... | | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | | Deposit date: | 2018-10-26 | | Release date: | 2019-04-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (6.9 Å) | | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
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8IB8
 | | Human TRiC-PhLP2A-actin complex in the closed state | | Descriptor: | ACTB protein (Fragment), Phosducin-like protein 3, T-complex protein 1 subunit alpha, ... | | Authors: | Roh, S.H, Park, J, Kim, H, Lim, S. | | Deposit date: | 2023-02-09 | | Release date: | 2023-12-20 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.42 Å) | | Cite: | A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle.
Nat Commun, 15, 2024
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8IHL
 | | Overlapping tri-nucleosome | | Descriptor: | DNA (353-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Nishimura, M, Fujii, T, Tanaka, H, Maehara, K, Nozawa, K, Takizawa, Y, Ohkawa, Y, Kurumizaka, H. | | Deposit date: | 2023-02-23 | | Release date: | 2024-01-17 | | Last modified: | 2024-01-24 | | Method: | ELECTRON MICROSCOPY (7.64 Å) | | Cite: | Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.
Commun Biol, 7, 2024
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6IEH
 | | Crystal structures of the hMTR4-NRDE2 complex | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, Exosome RNA helicase MTR4, ... | | Authors: | Chen, J.Y, Yun, C.H. | | Deposit date: | 2018-09-14 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.892 Å) | | Cite: | NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.
Genes Dev., 33, 2019
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6A5O
 | | RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Kujirai, T, Ehara, H, Fujino, Y, Shirouzu, M, Sekine, S, Kurumizaka, H. | | Deposit date: | 2018-06-25 | | Release date: | 2018-10-03 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (9.9 Å) | | Cite: | Structural basis of the nucleosome transition during RNA polymerase II passage.
Science, 362, 2018
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8I6J
 | | The focused refinement of CCT3-PhLP2A from TRiC-PhLP2A complex in the open state | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Phosducin-like protein 3, T-complex protein 1 subunit gamma | | Authors: | Roh, S.H, Park, J, Kim, H, Lim, S. | | Deposit date: | 2023-01-28 | | Release date: | 2024-01-31 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (3.82 Å) | | Cite: | A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle.
Nat Commun, 15, 2024
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8J6T
 | | Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome | | Descriptor: | Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B, Histone H3.1, ... | | Authors: | Liu, C.P, Yu, Z.Y, Xu, R.M. | | Deposit date: | 2023-04-26 | | Release date: | 2023-08-16 | | Last modified: | 2023-09-06 | | Method: | ELECTRON MICROSCOPY (6.6 Å) | | Cite: | Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1.
Science, 381, 2023
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8J6S
 | | Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome | | Descriptor: | Chromatin assembly factor 1 subunit A, Chromatin assembly factor 1 subunit B, Histone H3.1, ... | | Authors: | Liu, C.P, Yu, Z.Y, Xu, R.M. | | Deposit date: | 2023-04-26 | | Release date: | 2023-08-16 | | Last modified: | 2023-09-06 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1.
Science, 381, 2023
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6J50
 | | RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) | | Descriptor: | DNA (198-MER), DNA (41-MER), DNA-directed RNA polymerase subunit, ... | | Authors: | Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2019-01-10 | | Release date: | 2019-02-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (4.7 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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8JL9
 | | Cryo-EM structure of the human nucleosome with scFv | | Descriptor: | DNA (193-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.65 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLB
 | | Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-08 | | Method: | ELECTRON MICROSCOPY (2.36 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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8JLD
 | | Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail | | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | | Authors: | Oishi, T, Hatazawa, S, Kujirai, T, Kato, J, Kobayashi, Y, Ogasawara, M, Akatsu, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-02 | | Release date: | 2023-10-04 | | Last modified: | 2023-11-15 | | Method: | ELECTRON MICROSCOPY (2.48 Å) | | Cite: | Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51, 2023
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6J4W
 | | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2019-01-10 | | Release date: | 2019-02-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (7.9 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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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
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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
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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
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6JFB
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6J4Z
 | | RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome | | Descriptor: | DNA (198-MER), DNA (42-MER), DNA-directed RNA polymerase subunit, ... | | Authors: | Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2019-01-10 | | Release date: | 2019-02-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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8JNE
 | | The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding | | Descriptor: | DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... | | Authors: | Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2023-06-06 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.68 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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6J4X
 | | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) | | Descriptor: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Ehara, H, Kujirai, T, Fujino, Y, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2019-01-10 | | Release date: | 2019-02-20 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (4.3 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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