Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex)
Resolution: 7.14 Å
EM Method: Single-particle
Fitted PDBs: 9j8n
Q-score: 0.164
Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H
Nat Commun (2025) 16 pp. 1495-1495 [ Pubmed: 39929866 DOI: doi:10.1038/s41467-025-56823-9 ]
- Low mobility complex containing baf, lamin a/c igf, and nucleosome (620 kDa, Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Dna (193-mer) (59 kDa, DNA from synthetic construct)
- Barrier-to-autointegration factor (10 kDa, Protein from Homo sapiens)
- Lamin-a/c (17 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Overall map of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Dna (314-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
Map focused on RYBP/Ub of ncPRC1RYBP bound to asymmetric H2AK119Ub dinucleosome
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ DOI: doi:10.1038/s41586-024-08183-5 Pubmed: 39537923 ]
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Dna (314-mer) (Complex from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
Automethylated PRC2 dimer bound to nucleosome
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 8t9g
Q-score: 0.163
Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S
Mol Cell (2024) 84 pp. 3885-3898.e8 [ Pubmed: 39303719 DOI: doi:10.1016/j.molcel.2024.08.025 ]
- Proximal prc2 (Complex from Homo sapiens)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Distal prc2 (Complex from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Activating methylated peptide (1 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome
Resolution: 6.3 Å
EM Method: Single-particle
Fitted PDBs: 8uxq
Q-score: 0.143
To Be Published
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Hp1alpha dimer bound to h2a.z nucleosome (288 kDa, Complex from Escherichia coli)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromobox protein homolog 5 (22 kDa, Protein from Homo sapiens)
- Dna widom601 (208bp) strand2 (63 kDa, DNA from synthetic construct)
- Dna widom601 (208bp) strand1 (64 kDa, DNA from synthetic construct)
The cryo-EM structure of the RAD51 filament bound to the nucleosome
Resolution: 6.91 Å
EM Method: Single-particle
Fitted PDBs: 8jnf
Q-score: 0.143
Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H
Nature (2024) 628 pp. 212-220 [ DOI: doi:10.1038/s41586-024-07196-4 Pubmed: 38509361 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Dna repair protein rad51 homolog 1 (37 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (156-mer) (47 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rad51-nucleosome complex (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Resolution: 7.64 Å
EM Method: Single-particle
Fitted PDBs: 8ihl
Q-score: 0.109
Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H
Commun Biol (2024) 7 pp. 61-61 [ DOI: doi:10.1038/s42003-023-05694-1 Pubmed: 38191828 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (353-mer) (108 kDa, DNA from synthetic construct)
- Overlapping tri-nucleosome (511 kDa, Complex from Homo sapiens)
- Dna (353-mer) (109 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
Human CENP-A nucleosome assembled on alpha-satellite DNA (most unwrapped DNA)
Nagpal H, Ali-Ahmad A, Hirano Y, Cai W, Halic M, Fukagawa T, Sekulic N, Fierz B
Nat Commun (2023) 14 pp. 8227-8227 [ Pubmed: 38086807 DOI: doi:10.1038/s41467-023-43739-5 ]
- Human histone cenp-a (Protein from Homo sapiens)
- Human cenp-b (Protein from Homo sapiens)
- Human alpha-satellite dna (Protein from Homo sapiens)
- Human histone h2b (Protein from Homo sapiens)
- Human histone h4 (Protein from Homo sapiens)
- Human histone h2a (Protein from Homo sapiens)
- Human cenp-a nucleosome assembled on alpha-satellite dna (most unwrapped dna) (Complex from Homo sapiens)
Structure of TRF1core in complex with telomeric nucleosome (4:1 complex)
Hu H, van Roon AM, Ghanim GE, Ahsan B, Oluwole AO, Peak-Chew SY, Robinson CV, Nguyen THD
Sci Adv (2023) 9 pp. eadi4148-eadi4148 [ DOI: doi:10.1126/sciadv.adi4148 Pubmed: 37624885 ]
- Telomeric dna g strand (DNA from Homo sapiens)
- Human histone h3 (Protein from Homo sapiens)
- Human trf1 protein (Protein from Homo sapiens)
- Human histone h2a (Protein from Homo sapiens)
- Human trf1core complex (Complex from Homo sapiens)
- Human histone h2b (Protein from Homo sapiens)
- Human histone h4 (Protein from Homo sapiens)
- Human telomeric nucleosome (Complex from Homo sapiens)
- Telomeric dna c strand (DNA from Homo sapiens)
- Trf1core in complex with telomeric nucleosome (Complex)
Resolution: 7.1 Å
EM Method: Single-particle
Fitted PDBs: 7wbw
Q-score: 0.137
Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H
J Mol Biol (2023) 435 pp. 168130-168130 [ DOI: doi:10.1016/j.jmb.2023.168130 Pubmed: 37120012 ]
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Dna, rna (Complex)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5 (Complex from Homo sapiens)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone (Complex)
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor spt5 (101 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-3.5) of the nucleosome (Complex from Komagataella phaffii)
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Rna (5'-r(p*gp*up*up*up*up*cp*gp*up*up*gp*up*up*up*up*up*u)-3') (4 kDa, RNA from synthetic construct)