7PF3
 
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7PF4
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7PF6
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8SNA
 | | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) | | Descriptor: | DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... | | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | | Deposit date: | 2023-04-26 | | Release date: | 2024-01-17 | | Last modified: | 2024-03-20 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation.
Mol.Cell, 84, 2024
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6R93
 | | Cryo-EM structure of NCP-6-4PP | | Descriptor: | Histone H2A type 1-B/E, Histone H2B type 1-J, Histone H3.1, ... | | 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 Å) | | Cite: | DNA damage detection in nucleosomes involves DNA register shifting.
Nature, 571, 2019
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6T7C
 | | Structure of two copies of human Sox11 transcription factor in complex with a nucleosome | | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | | Authors: | Dodonova, S.O, Zhu, F, Dienemann, C, Taipale, J, Cramer, P. | | Deposit date: | 2019-10-21 | | Release date: | 2020-04-29 | | Last modified: | 2024-05-22 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Nature, 580, 2020
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4YM5
 | | Crystal structure of the human nucleosome containing 6-4PP (inside) | | Descriptor: | 144 mer-DNA, 144-mer DNA, Histone H2A type 1-B/E, ... | | Authors: | Osakabe, A, Tachiwana, H, Kagawa, W, Horikoshi, N, Matsumoto, S, Hasegawa, M, Matsumoto, N, Toga, T, Yamamoto, J, Hanaoka, F, Thoma, N.H, Sugasawa, K, Iwai, S, Kurumizaka, H. | | Deposit date: | 2015-03-06 | | Release date: | 2015-12-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4.005 Å) | | Cite: | Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome
Sci Rep, 5, 2015
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7XZZ
 | | Cryo-EM structure of the nucleosome in complex with p53 | | Descriptor: | Cellular tumor antigen p53, DNA (169-MER), Histone H2A type 1-B/E, ... | | Authors: | Nishimura, M, Nozawa, K, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-12 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (4.07 Å) | | Cite: | Structural basis for p53 binding to its nucleosomal target DNA sequence.
Pnas Nexus, 1, 2022
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7WBV
 | | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome | | Descriptor: | DNA (159-MER), DNA (198-MER), DNA-directed RNA polymerase subunit, ... | | Authors: | Osumi, K, Kujirai, T, Ehara, H, Sekine, S, Takizawa, Y, Kurumizaka, H. | | Deposit date: | 2021-12-17 | | Release date: | 2023-07-05 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome.
J.Mol.Biol., 435, 2023
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7SCY
 | | Nuc147 bound to single BRCT | | Descriptor: | DNA (147-MER), Histone H2A, Histone H2B type 1-J, ... | | Authors: | Muthurajan, U.M, Rudolph, J.R. | | Deposit date: | 2021-09-29 | | Release date: | 2022-01-12 | | Last modified: | 2024-06-05 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer.
Mol.Cell, 81, 2021
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8EVJ
 | | CX3CR1 nucleosome bound PU.1 and C/EBPa | | Descriptor: | DNA (167-MER), Histone H2A type 2-C, Histone H2B type 2-E, ... | | Authors: | Guan, R, Bai, Y, Lian, T. | | Deposit date: | 2022-10-20 | | Release date: | 2023-11-01 | | Last modified: | 2024-05-01 | | Method: | ELECTRON MICROSCOPY (4.1 Å) | | Cite: | Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha.
Nat.Struct.Mol.Biol., 31, 2024
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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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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
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8XBT
 | | The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with 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: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.12 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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7XT7
 | | RNA polymerase II elongation complex transcribing a nucleosome (EC49B) | | Descriptor: | Component of the Paf1p complex, Constituent of Paf1 complex with RNA polymerase II, Paf1p, ... | | Authors: | Ehara, H, Kujirai, T, Shirouzu, M, Kurumizaka, H, Sekine, S. | | Deposit date: | 2022-05-16 | | Release date: | 2022-10-12 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.
Science, 377, 2022
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8HAN
 | | Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 | | Descriptor: | CREB-binding protein, DNA (180-mer), Histone H2A type 1-B/E, ... | | Authors: | Kikuchi, M, Morita, S, Wakamori, M, Shin, S, Uchikubo-Kamo, T, Shirouzu, M, Umehara, T. | | Deposit date: | 2022-10-26 | | Release date: | 2023-05-17 | | Last modified: | 2023-07-26 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Epigenetic mechanisms to propagate histone acetylation by p300/CBP.
Nat Commun, 14, 2023
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7BXT
 | | The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain | | Descriptor: | CENP-C, DNA (145-mer), Histone H2A type 1-B/E, ... | | Authors: | Ariyoshi, M, Makino, F, Fukagawa, T. | | Deposit date: | 2020-04-20 | | Release date: | 2021-02-10 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (4.2 Å) | | Cite: | Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C.
Embo J., 40, 2021
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6J51
 | | RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) | | Descriptor: | DNA (198-MER), DNA (36-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 (4.2 Å) | | Cite: | Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science, 363, 2019
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8XBU
 | | The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with 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: | 2023-12-07 | | Release date: | 2024-03-27 | | Last modified: | 2024-05-08 | | Method: | ELECTRON MICROSCOPY (4.24 Å) | | Cite: | Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site.
Nature, 628, 2024
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7PFX
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7PFF
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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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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
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6J4Y
 | | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) | | 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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7BWD
 | | Structure of Dot1L-H2BK34ub Nucleosome Complex | | Descriptor: | DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | | Authors: | Lou, Z.Y, Liu, L, Cao, L, Ai, H.S, Sun, Z.X. | | Deposit date: | 2020-04-14 | | Release date: | 2021-04-14 | | Method: | ELECTRON MICROSCOPY (4.32 Å) | | Cite: | Structure of the Dot1L-H2BK34ub Nucleosome Complex Reveals an Unprecedented Crosstalk Activation Mechanism through Nucleosome Shape Distortion
To Be Published
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