Human menin in complex with H3K79Me2 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8gpn
Q-score: 0.459
Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD
Science (2023) 379 pp. 717-723 [ DOI: doi:10.1126/science.adc9318 Pubmed: 36795828 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Nh3k79 dimethylated nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Isoform 2 of menin (67 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (177-mer) (Complex from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from Homo sapiens)
- Human menin in complex with nh3k79 dimethylated nucleosome (300 kDa, Complex from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Isoform 2 of menin (Complex)
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 [ Pubmed: 34643712 DOI: doi:10.1093/nar/gkab907 ]
- Histone h3 (Complex from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Dna (136-mer) (45 kDa, DNA from unidentified)
- Dna (136-mer) (45 kDa, DNA from unidentified)
- Nucleosome core particle containing variant h2a.z and canonical core histones (Complex)
- Histone variant h2a.z (Complex from Mus musculus)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (136-mer) (Complex from unidentified)
- Histone h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 ]
- 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)
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7kbd
Q-score: 0.489
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nucleosome in interphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7kbe
Q-score: 0.445
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Xenopus laevis)
- Nucleosome isolated from metaphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6zhx
Q-score: 0.625
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Crosslinked complex of alc1 regulatory linker and the nucleosome (206 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Water (18 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6zhy
Q-score: 0.516
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- A hexasome (nucleosome lacking one of the two h2a-h2b dimers) with its acidic patch bound by the alc1 linker regulatory region. (170 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
Nucleosome-CHD4 complex structure (single CHD4 copy)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ryr
Q-score: 0.52
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56178 Pubmed: 32543371 ]
- Zinc ion (65 Da, Ligand)
- Nucleosome-chd4 complex (Complex)
- Chd4 (Complex from Homo sapiens)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (149-mer) (46 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
Nucleosome-CHD4 complex structure (two CHD4 copies)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6ryu
Q-score: 0.342
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56178 Pubmed: 32543371 ]
- Zinc ion (65 Da, Ligand)
- Nucleosome-chd4 complex (Complex)
- Histone (Complex from Xenopus laevis)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (149-mer) (46 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 4 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Chromodomain-helicase-dna-binding protein 4,chd4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
SWI/SNF nucleosome complex with ADP-BeFx
Resolution: 8.96 Å
EM Method: Single-particle
Fitted PDBs: 6uxw
Q-score: 0.122
Han Y, Reyes AA, Malik S, He Y
Nature (2020) 579 pp. 452-455 [ DOI: doi:10.1038/s41586-020-2087-1 Pubmed: 32188938 ]
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf2 (194 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf complex subunit swi3 (93 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae S288C)
- 601 sequence bottom strand (56 kDa, DNA from synthetic construct)
- Phosphate ion (94 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf6 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swi/snf chromatin-remodeling complex subunit snf5 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf global transcription activator complex subunit swp82 (7 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Water (18 Da, Ligand)
- 601 sequence top strand (61 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf nucleosome complex with adp-befx (Complex from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Swi/snf chromatin-remodeling complex subunit swi1 (148 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))