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Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8u5h
Q-score: 0.443
To Be Published
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dnmt3a n-terminal domain and h2ak119ub nucleosome complex (Complex from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome
Jung H, Sokolova V, Lee G, Stevens VR, Tan D
Epigenomes (2024) [ DOI: doi:10.3390/epigenomes8020021 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Nucleosome containing histone variants h3.3 and h2a.z (288 kDa, Complex from Escherichia coli)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Dna (128-mer) (45 kDa, DNA from synthetic construct)
- Dna (128-mer) (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 0
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Widom 601 reverse dna (DNA from synthetic construct)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 1
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Widom 601 reverse dna (DNA from synthetic construct)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 2
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Widom 601 reverse dna (DNA from synthetic construct)
Cryo-EM structure of yeast SWR1C subunit Swc5 bound to the nucleosome, 3D class 4
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL
eLife (2024) 13 [ Pubmed: 38809771 DOI: doi:10.7554/eLife.94869 ]
- Histone h2a.1 (Protein from Saccharomyces cerevisiae)
- Widom 601 forward dna (DNA from synthetic construct)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swr1-complex protein 5 (Protein from Saccharomyces cerevisiae)
- Histone h2b.1 (Protein from Saccharomyces cerevisiae)
- Swc5 in complex with nucleosome core particle (Complex from Xenopus laevis)
- Widom 601 reverse dna (DNA from synthetic construct)
Human canonical 601 DNA nucleosome
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8jbx
Q-score: 0.43
Ding DB, Ishibashi T, Nguyen TT
To Be Published
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- 601 dna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone and 601 dna (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 8jcc
Q-score: 0.398
To Be Published
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- H2bfwt nucleosome (Complex from Homo sapiens)
Human H2BFWTH100R nucleosome with 601 DNA
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8jcd
Q-score: 0.445
Ding DB, Ishibashi T, Nguyen TT
To Be Published
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- 601 dna (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type w-t (16 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Human canonical histone and 601 dna (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w9d
Q-score: 0.263
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)