Electron Microscopy Data Bank

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1)

Release date: Jan. 17, 2024
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8sn3
Q-score: 0.429

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40612

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2)

Release date: Jan. 17, 2024
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn4
Q-score: 0.439

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40613

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3)

Release date: Jan. 17, 2024
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8sn5
Q-score: 0.41

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40614

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4)

Release date: Jan. 17, 2024
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn6
Q-score: 0.434

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40615

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5)

Release date: Jan. 17, 2024
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn7
Q-score: 0.445

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40616

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Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6)

Release date: Jan. 17, 2024
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn8
Q-score: 0.443

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40617

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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 1)

Release date: Jan. 17, 2024
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8sn9
Q-score: 0.424

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (with backside ub) (256 kDa, Complex from Homo sapiens)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-40618

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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)

Release date: Jan. 17, 2024
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8sna
Q-score: 0.405

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Zinc ion (65 Da, Ligand)
Human nucleosome core particle in complex with rnf168 and ubch5c~ub (with backside ub) (256 kDa, Complex from Homo sapiens)
Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-41706

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Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1)

Release date: Jan. 17, 2024
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8txv
Q-score: 0.432

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-c/e/f/g/i (14 kDa, Protein from Homo sapiens)
Human nucleosome core particle ubiquitylated at histone h2a k15 in complex with rnf168 (class 1) (280 kDa, Complex from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (66 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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EMD-41707

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Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2)

Release date: Jan. 17, 2024
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8txw
Q-score: 0.455

Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G

Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]

Sample:

Histone h2b type 1-c/e/f/g/i (14 kDa, Protein from Homo sapiens)
E3 ubiquitin-protein ligase rnf168 (66 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
Histone h3.1 (15 kDa, Protein from Homo sapiens)
Human nucleosome core particle ubiquitylated at histone h2a k15 in complex with rnf168 (class 2) (280 kDa, Complex from Homo sapiens)
Histone h4 (11 kDa, Protein from Homo sapiens)
Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
Dna (147-mer) (45 kDa, DNA from Homo sapiens)

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