8TXW
| Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (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: | 2023-08-24 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8U13
| Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) | Descriptor: | DNA (146-MER), DNA (147-MER), E3 ubiquitin-protein ligase RNF168, ... | Authors: | Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. | Deposit date: | 2023-08-30 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8UQ8
| Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker | Descriptor: | CHLORIDE ION, E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E, GLYCEROL, ... | Authors: | Hu, Q, Botuyan, M.V, Mer, G. | Deposit date: | 2023-10-23 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8UQD
| Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) | Descriptor: | E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E | Authors: | Hu, Q, Botuyan, M.V, Mer, G. | Deposit date: | 2023-10-23 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3.893 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8UQC
| Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) | Descriptor: | E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E, ZINC ION | Authors: | Hu, Q, Botuyan, M.V, Mer, G. | Deposit date: | 2023-10-23 | Release date: | 2024-01-17 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.61 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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7YBF
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8CBN
| structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome | Descriptor: | Histone H2A, Histone H2B 1.1, Histone H3, ... | Authors: | Koutna, E, Kouba, T, Novacek, J, Veverka, V. | Deposit date: | 2023-01-25 | Release date: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (3.34 Å) | Cite: | Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res., 51, 2023
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8WG5
| Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | Authors: | Ai, H.S, He, Z.Z, Deng, Z.H, Liu, L. | Deposit date: | 2023-09-20 | Release date: | 2023-12-27 | Last modified: | 2024-07-10 | Method: | ELECTRON MICROSCOPY (3.05 Å) | Cite: | Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Nat.Struct.Mol.Biol., 2024
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7YRG
| histone methyltransferase | Descriptor: | DNA (146-MER), Histone H2A.Z, Histone H2B 1.1, ... | Authors: | Li, H, Wang, W.Y. | Deposit date: | 2022-08-09 | Release date: | 2023-12-13 | Method: | ELECTRON MICROSCOPY (4.2 Å) | Cite: | Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1. Mol.Cell, 83, 2023
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7XYF
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7XYG
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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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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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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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8UX1
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8JHG
| Native SUV420H1 bound to 167-bp nucleosome | Descriptor: | DNA (160-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | Authors: | Lin, F, Li, W. | Deposit date: | 2023-05-23 | Release date: | 2023-11-22 | Last modified: | 2023-12-20 | Method: | ELECTRON MICROSCOPY (3.58 Å) | Cite: | Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase. Cell Discov, 9, 2023
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8JHF
| Native SUV420H1 bound to 167-bp nucleosome | Descriptor: | DNA (160-MER), Histone H2A.Z, Histone H2B type 1-K, ... | Authors: | Lin, F, Li, W. | Deposit date: | 2023-05-23 | Release date: | 2023-11-15 | Last modified: | 2023-12-20 | Method: | ELECTRON MICROSCOPY (3.68 Å) | Cite: | Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase. Cell Discov, 9, 2023
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7XFJ
| Structure of nucleosome-AAG complex (T-50I, post-catalytic state) | Descriptor: | DNA (152-MER), DNA-3-methyladenine glycosylase, Histone H2A type 1, ... | Authors: | Zheng, L, Tsai, B, Gao, N. | Deposit date: | 2022-04-01 | Release date: | 2023-11-08 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome. Cell Discov, 9, 2023
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8SYP
| Genomic CX3CR1 nucleosome | Descriptor: | DNA (162-MER), Histone H2A type 2-C, Histone H2B type 2-E, ... | Authors: | Lian, T, Guan, R, Bai, Y. | Deposit date: | 2023-05-25 | Release date: | 2023-11-01 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.6 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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8EVG
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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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8EVI
| CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations | Descriptor: | DNA (167-MER), Histone H2A type 2-C, Histone H2B type 2-E, ... | Authors: | Lian, T, Guan, R, Bai, Y. | Deposit date: | 2022-10-20 | Release date: | 2023-11-01 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.64 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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8EVH
| CX3CR1 nucleosome and wild type PU.1 complex | Descriptor: | DNA (162-MER), Histone H2A type 2-C, Histone H2B type 2-E, ... | Authors: | Lian, T, Guan, R, Bai, Y. | Deposit date: | 2022-10-20 | Release date: | 2023-11-01 | Last modified: | 2024-05-01 | Method: | ELECTRON MICROSCOPY (2.85 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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8T3W
| Structure of Bre1-nucleosome complex - state2 | Descriptor: | 601 DNA strand 1, 601 DNA strand 2, E3 ubiquitin-protein ligase BRE1, ... | Authors: | Zhao, F, Hicks, C.W, Wolberger, C. | Deposit date: | 2023-06-07 | Release date: | 2023-10-18 | Last modified: | 2023-11-22 | Method: | ELECTRON MICROSCOPY (3.25 Å) | Cite: | Mechanism of histone H2B monoubiquitination by Bre1. Nat.Struct.Mol.Biol., 30, 2023
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8T3Y
| Structure of Bre1-nucleosome complex - state1 | Descriptor: | 601 DNA Strand 1, 601 DNA Strand 2, E3 ubiquitin-protein ligase BRE1, ... | Authors: | Zhao, F, Hicks, C.W, Wolberger, C. | Deposit date: | 2023-06-08 | Release date: | 2023-10-18 | Last modified: | 2023-11-22 | Method: | ELECTRON MICROSCOPY (3.47 Å) | Cite: | Mechanism of histone H2B monoubiquitination by Bre1. Nat.Struct.Mol.Biol., 30, 2023
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