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
Chen X, Guo Y, Zhao T, Lu J, Fang J, Wang Y, Wang GG, Song J
Nat Commun (2024) 15 pp. 6217-6217 [ Pubmed: 39043678 DOI: doi:10.1038/s41467-024-50526-3 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h3.3c (15 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (11 kDa, Protein from Homo sapiens)
- Nucleosome dna (55 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dnmt3a n-terminal domain and h2ak119ub nucleosome complex (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
Cryo-EM structure of SNF2h-nucleosome complex (consensus structure)
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Snf2h (Complex from Homo sapiens)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (Protein from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna reverse (DNA from synthetic construct)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna forward (DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (100 kDa, Complex from Homo sapiens)
- Nucleosome with xenopus laevis histones (Complex from Xenopus laevis)
Cryo-EM structure of SNF2h-nucleosome complex (single-bound structure)
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna reverse strand (DNA from synthetic construct)
- Histone h3.2 (Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (Protein from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Widom 601 dna (147-mer) plus 60 base pairs flanking dna forward strand (DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Snf2h (100 kDa, Complex from Homo sapiens)
Cryo-EM structure of doubly-bound SNF2h-nucleosome complex (conformation 1)
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (DNA from synthetic construct)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (Protein from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Snf2h (100 kDa, Complex from Homo sapiens)
Cryo-EM structure of doubly-bound SNF2h-nucleosome complex (conformation 2)
Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y
Nat Commun (2024) 15 pp. 2225-2225 [ Pubmed: 38472177 DOI: doi:10.1038/s41467-024-46178-y ]
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (forward strand) (DNA from synthetic construct)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily a member 5 (Protein from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Widom 601 dna (147-mer) with 60 base pairs flanking dna (reverse strand) (DNA from synthetic construct)
- Atp-dependent chromatin remodeler snf2h in complex with nucleosome (300 kDa, Complex)
- Nucleosome with xenopus laevis histones (200 kDa, Complex)
- Snf2h (100 kDa, Complex from Homo sapiens)
Rpd3S bound to an H3K36Cme3 modified nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8tof
Q-score: 0.464
Nat Commun (2023) 14 pp. 8128-8128 [ DOI: doi:10.1038/s41467-023-43968-8 Pubmed: 38065958 ]
- Zinc ion (65 Da, Ligand)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b0a
Q-score: 0.483
Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S
Nat Commun (2024) 15 pp. 1000-1000 [ Pubmed: 38307862 DOI: doi:10.1038/s41467-024-45237-8 ]
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Complex between alc1 and a site-specifically parylated nucleosome (304 kDa, Complex from Homo sapiens)
The structure of ALC1 bound to the nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7enn
Q-score: 0.567
Nat Commun (2021) 12 pp. 4057-4057 [ Pubmed: 34210977 DOI: doi:10.1038/s41467-021-24320-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Histone (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Alc1 (Complex from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- The structure of alc1 bound to the nucleosome (Complex)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (101 kDa, Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6w5i
Q-score: 0.135
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6w5m
Q-score: 0.177
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)