Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01
Ayoub A, Park SH, Lee YT, Cho US, Dou Y
Biochemistry (2022) 61 pp. 1-9 [ Pubmed: 34928138 DOI: doi:10.1021/acs.biochem.1c00603 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Rbbp5, wdr5, set1, and ash2l (Complex from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (mode01) (Complex)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02
Ayoub A, Park SH, Lee YT, Cho US, Dou Y
Biochemistry (2022) 61 pp. 1-9 [ Pubmed: 34928138 DOI: doi:10.1021/acs.biochem.1c00603 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Rbbp5, wdr5, set1, and ash2l (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (mode02) (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
NSD2 E1099K mutant bound to nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7e8d
Q-score: 0.556
Sato K, Kumar A, Hamada K, Okada C, Oguni A, Machiyama A, Sakuraba S, Nishizawa T, Nureki O, Kono H, Ogata K, Sengoku T
Nat Commun (2021) 12 pp. 6605-6605 [ DOI: doi:10.1038/s41467-021-26913-5 Pubmed: 34782608 ]
- Dna (185-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Sinefungin (381 Da, Ligand)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Nsd2-nucleosome complex (Complex from Homo sapiens)
- Dna (185-mer) (56 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase nsd2 (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
CHD7 N-CRD and nucleosome(+40bp) complex
Lee E, Kang C, Purhonen P, Hebert H, Bouazoune K, Hohng S, Song JJ
J Mol Biol (2021) 433 pp. 167114-167114 [ DOI: doi:10.1016/j.jmb.2021.167114 Pubmed: 34161779 ]
- Histone (Complex from Xenopus laevis)
- Chd7 n-crd (Macromolecule from Homo sapiens)
- Histone h2a (Macromolecule from Xenopus laevis)
- Dna (Complex)
- Histone h4 (Macromolecule from Xenopus laevis)
- Histone h3 (Macromolecule from Xenopus laevis)
- Histone h2b (Macromolecule from Xenopus laevis)
- Widom 601 dna with extra 40bp of vector sequence (RNA from synthetic construct)
- Cryo em structure of chd7 n-crd bound to the nucleosome (Complex)
- Chd7 n-crd (Complex from Homo sapiens)
cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7m1x
Q-score: 0.391
Lewis TS, Sokolova V, Jung H, Ng H, Tan D
Nucleic Acids Res (2021) 49 pp. 11379-11391 [ DOI: doi:10.1093/nar/gkab907 Pubmed: 34643712 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone variant h2a.z (Complex from Mus musculus)
- Nucleosome core particle containing variant h2a.z and canonical core histones (Complex)
- Histone h4 (Complex from Xenopus laevis)
- Histone h3 (Complex from Xenopus laevis)
- Dna (136-mer) (45 kDa, DNA from unidentified)
- Dna (136-mer) (Complex from unidentified)
- Dna (136-mer) (45 kDa, DNA from unidentified)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (Complex from Xenopus laevis)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
H2A.Z Dodecanucleosome 30 nm Fiber
Lewis TS, Sokolova V, Jung H, Ng H, Tan D
Nucleic Acids Res (2021) 49 pp. 11379-11391 [ DOI: doi:10.1093/nar/gkab907 Pubmed: 34643712 ]
- Histone h2a.z (Complex from Mus musculus)
- In vitro reconstituted 12x167 bp chromatin (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b (Protein from Xenopus laevis)
- Histone h3 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histone h2a.z (Protein from Mus musculus)
- Histone h3 (Complex from Xenopus laevis)
- 12 tandem repeats of 167 bp of 601 windom nucleosome-positioning sequence (Complex from unidentified)
- Histone h2b (Complex from Xenopus laevis)
- 12 tandem repeats of 167 bp of 601 windom nucleosome-positioning sequence (DNA from unidentified)
cryo-EM density map of chromatin fiber containing canonical histones and 167-bp 601 DNA
Lewis TS, Sokolova V, Jung H, Ng H, Tan D
Nucleic Acids Res (2021) 49 pp. 11379-11391 [ DOI: doi:10.1093/nar/gkab907 Pubmed: 34643712 ]
- Histone h3 (Protein from Xenopus laevis)
- Histones h2a (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3 (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- 12x167bp 601 dna (Complex from unidentified)
- In-vitro reconstituted chromatin fiber containing canonical histones and twelve tandem repeats of 167-bp 601 windom sequence (Complex from Xenopus laevis)
- Histone h2b (Complex from Xenopus laevis)
- 12x 167bp 601 dna (DNA from unidentified)
cryo-EM density map of canonical nucleosome
Lewis TS, Sokolova V, Jung H, Ng H, Tan D
Nucleic Acids Res (2021) 49 pp. 11379-11391 [ DOI: doi:10.1093/nar/gkab907 Pubmed: 34643712 ]
- Nucleosome containing canonical histones h2a, h2b, h3 and h4 (Complex from Xenopus laevis)
- Histone h3 (Protein from Xenopus laevis)
- Histones h2a (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3 (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- 167-bp 601 widom dna sequence (DNA from unidentified)
- Histone h2b (Complex from Xenopus laevis)
- 167-bp 601 widom dna sequence (Complex from unidentified)
Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7otq
Q-score: 0.282
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton S, Deindl S, Workman JL
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
cryoDRGN graph traversal of the ALC1 - PARylated nucleosome complex particle distribution
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton S, Deindl S
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Widom 601 sequence (DNA from synthetic construct)
- Histone (Complex from Xenopus laevis)
- Alc1/chd1l (Protein from Homo sapiens)
- Alc1/chd1l (Complex from Homo sapiens)
- Histone h3 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex)
- Histone h2b (Protein from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- Widom 601 sequence (Complex from synthetic construct)