8KB5
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![BU of 8kb5 by Molmil](/molmil-images/mine/8kb5) | Cryo-EM structure of the human nucleosome containing H3.8 | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Hirai, H, Kujirai, T, Takizawa, Y, Kurumizaka, H. | Deposit date: | 2023-08-03 | Release date: | 2023-10-18 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (2.26133 Å) | Cite: | Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8. J.Biochem., 174, 2023
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8UQ9
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![BU of 8uq9 by Molmil](/molmil-images/mine/8uq9) | Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-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 (2.3 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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8Q3X
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![BU of 8q3x by Molmil](/molmil-images/mine/8q3x) | Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) | Descriptor: | 4-diphenylphosphanylbenzoic acid, DNA (145-MER), GOLD ION, ... | Authors: | De Falco, L, Batchelor, L.K, Dyson, P.J, Davey, C.A. | Deposit date: | 2023-08-04 | Release date: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.301 Å) | Cite: | Viral peptide conjugates for metal-warhead delivery to chromatin. Rsc Adv, 14, 2024
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8UQ8
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![BU of 8uq8 by Molmil](/molmil-images/mine/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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5B32
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![BU of 5b32 by Molmil](/molmil-images/mine/5b32) | The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Horikoshi, N, Taguchi, H, Arimura, Y, Kurumizaka, H. | Deposit date: | 2016-02-08 | Release date: | 2016-08-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A. Open Biology, 6, 2016
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3UGB
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![BU of 3ugb by Molmil](/molmil-images/mine/3ugb) | UbcH5c~Ubiquitin Conjugate | Descriptor: | GLYCEROL, Polyubiquitin-C, Ubiquitin-conjugating enzyme E2 D3 | Authors: | Page, R.C, Pruneda, J.N, Klevit, R.E, Misra, S. | Deposit date: | 2011-11-02 | Release date: | 2012-05-16 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Structural insights into the conformation and oligomerization of E2~ubiquitin conjugates. Biochemistry, 51, 2012
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8JLB
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![BU of 8jlb by Molmil](/molmil-images/mine/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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6KBB
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![BU of 6kbb by Molmil](/molmil-images/mine/6kbb) | Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition | Descriptor: | Histone H2A type 1-D, Histone H2B type 2-E, SWR1-complex protein 5 | Authors: | Huang, Y, Zhou, Z. | Deposit date: | 2019-06-24 | Release date: | 2020-01-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.365 Å) | Cite: | Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing. Proc.Natl.Acad.Sci.USA, 117, 2020
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5AVB
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![BU of 5avb by Molmil](/molmil-images/mine/5avb) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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8AMS
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![BU of 8ams by Molmil](/molmil-images/mine/8ams) | Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin | Descriptor: | 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL, GLYCEROL, Polyubiquitin-C, ... | Authors: | Perez-Borrajero, C, Kotova, I, Murciano, B, Hennig, J. | Deposit date: | 2022-08-04 | Release date: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural and biophysical studies of TRIM2 and TRIM3 To Be Published
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3AZG
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![BU of 3azg by Molmil](/molmil-images/mine/3azg) | Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation | Descriptor: | 146-MER DNA, CHLORIDE ION, Histone H2A type 1-B/E, ... | Authors: | Iwasaki, W, Tachiwana, H, Kawaguchi, K, Shibata, T, Kagawa, W, Kurumizaka, H. | Deposit date: | 2011-05-25 | Release date: | 2011-09-21 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains Biochemistry, 50, 2011
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6JR1
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![BU of 6jr1 by Molmil](/molmil-images/mine/6jr1) | Crystal structure of the human nucleosome phased with 16 selenium atoms | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Saotome, M, Horikoshi, N, Urano, K, Kujirai, T, Yuzurihara, H, Kurumizaka, H, Kagawa, W. | Deposit date: | 2019-04-02 | Release date: | 2019-10-02 | Last modified: | 2019-10-23 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structure determination of the nucleosome core particle by selenium SAD phasing. Acta Crystallogr D Struct Biol, 75, 2019
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5AV5
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![BU of 5av5 by Molmil](/molmil-images/mine/5av5) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-11 | Release date: | 2015-12-23 | Last modified: | 2020-02-19 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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5AVC
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![BU of 5avc by Molmil](/molmil-images/mine/5avc) | human nucleosome core particle | Descriptor: | DNA (147-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Wakamori, M, Fujii, Y, Umehara, T, Yokoyama, S. | Deposit date: | 2015-06-12 | Release date: | 2015-12-23 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation Sci Rep, 5, 2015
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8JLD
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![BU of 8jld by Molmil](/molmil-images/mine/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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8UQB
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![BU of 8uqb by Molmil](/molmil-images/mine/8uqb) | Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) | Descriptor: | CHLORIDE ION, 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 (2.484 Å) | Cite: | Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
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5JRG
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![BU of 5jrg by Molmil](/molmil-images/mine/5jrg) | Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) | Descriptor: | CHLORIDE ION, DNA (145-MER), Histone H2A type 1-B/E, ... | Authors: | Osakabe, A, Arimura, Y, Horikoshi, N, Kurumizaka, H. | Deposit date: | 2016-05-06 | Release date: | 2017-03-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Polymorphism of apyrimidinic DNA structures in the nucleosome Sci Rep, 7, 2017
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6L9Z
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![BU of 6l9z by Molmil](/molmil-images/mine/6l9z) | 338 bp di-nucleosome assembled with linker histone H1.X | Descriptor: | CALCIUM ION, CHLORIDE ION, DNA (338-MER), ... | Authors: | Adhireksan, Z, Sharma, D, Lee, P.L, Davey, C.A. | Deposit date: | 2019-11-11 | Release date: | 2021-02-17 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Res., 49, 2021
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3AFA
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![BU of 3afa by Molmil](/molmil-images/mine/3afa) | The human nucleosome structure | Descriptor: | 146-MER DNA, CHLORIDE ION, Histone H2A type 1-B/E, ... | Authors: | Tachiwana, H, Kagawa, W, Osakabe, A, Koichiro, K, Shiga, T, Kimura, H, Kurumizaka, H. | Deposit date: | 2010-02-24 | Release date: | 2010-05-26 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T Proc.Natl.Acad.Sci.USA, 107, 2010
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3AV1
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![BU of 3av1 by Molmil](/molmil-images/mine/3av1) | The human nucleosome structure containing the histone variant H3.2 | Descriptor: | 146-MER DNA, Histone H2A type 1-B/E, Histone H2B type 1-J, ... | Authors: | Tachiwana, H, Osakabe, A, Shiga, T, Miya, Y, Kimura, H, Kagawa, W, Kurumizaka, H. | Deposit date: | 2011-02-18 | Release date: | 2011-06-01 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structures of human nucleosomes containing major histone H3 variants Acta Crystallogr.,Sect.D, 67, 2011
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6JR0
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![BU of 6jr0 by Molmil](/molmil-images/mine/6jr0) | Crystal structure of the human nucleosome phased with 12 selenium atoms | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Saotome, M, Horikoshi, N, Urano, K, Kujirai, T, Yuzurihara, H, Kurumizaka, H, Kagawa, W. | Deposit date: | 2019-04-02 | Release date: | 2019-10-02 | Last modified: | 2019-10-23 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structure determination of the nucleosome core particle by selenium SAD phasing. Acta Crystallogr D Struct Biol, 75, 2019
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2CV5
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![BU of 2cv5 by Molmil](/molmil-images/mine/2cv5) | Crystal structure of human nucleosome core particle | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A.a, ... | Authors: | Tsunaka, Y, Kajimura, N, Tate, S, Morikawa, K. | Deposit date: | 2005-05-31 | Release date: | 2005-06-28 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle Nucleic Acids Res., 33, 2005
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8Q3M
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![BU of 8q3m by Molmil](/molmil-images/mine/8q3m) | Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution | Descriptor: | DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-K, ... | Authors: | De Falco, L, Batchelor, L.K, Dyson, P.J, Davey, C.A. | Deposit date: | 2023-08-04 | Release date: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.503 Å) | Cite: | Viral peptide conjugates for metal-warhead delivery to chromatin. Rsc Adv, 14, 2024
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5YDK
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![BU of 5ydk by Molmil](/molmil-images/mine/5ydk) | Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form | Descriptor: | E3 ubiquitin-protein ligase RNF168, GLYCEROL, Ubiquitin-40S ribosomal protein S27a | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | Deposit date: | 2017-09-13 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.505 Å) | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168 Nat Commun, 9, 2018
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5B0Y
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![BU of 5b0y by Molmil](/molmil-images/mine/5b0y) | Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 | Descriptor: | CHLORIDE ION, DNA (146-MER), Histone H2A type 1-B/E, ... | Authors: | Suzuki, Y, Horikoshi, N, Kurumizaka, H. | Deposit date: | 2015-11-13 | Release date: | 2016-01-27 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.557 Å) | Cite: | Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122 Biochem.Biophys.Res.Commun., 469, 2016
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