Resolution: 7.8 Å
EM Method: Single-particle
Fitted PDBs: 9mu9
Q-score: 0.202
Venette-Smith NL, Vishwakarma RK, Dollinger R, Schultz J, Venkatakrishnan V, Babitzke P, Anand G, Gilmour DS, Armache J-P, Murakami K
To Be Published
- Non-template dna (50 kDa, DNA from Drosophila melanogaster)
- Rna (3 kDa, RNA from Drosophila melanogaster)
- Template dna (53 kDa, DNA from Drosophila melanogaster)
- Histone h3 (11 kDa, Protein from Drosophila melanogaster)
- Histone h4 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb5 (24 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (9 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Histone h2b (10 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb12 (5 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Drosophila melanogaster)
- Native purified nucleosome elongation complex from drosophila melanogaster (750 kDa, Complex from Drosophila melanogaster)
- Histone h2a (11 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb2 (132 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb1 (166 kDa, Protein from Drosophila melanogaster)
- Dna-directed rna polymerase ii subunit rpb9 (13 kDa, Protein from Drosophila melanogaster)
Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8rup
Q-score: 0.551
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
Borealin N-terminus in complex with H3.T3p-nucleosome
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 8ruq
Q-score: 0.618
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (47 kDa, DNA from unidentified)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromosome passenger complex localisation module (borealin n-terminus only) (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Dna (147-mer) (46 kDa, DNA from unidentified)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
Cryo-EM structure of nucleosome containing Widom603 DNA
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8rgm
Q-score: 0.352
Motorin NA, Afonin D, Armeev GA, Moiseenko A, Zhao L, Vasiliev V, Oleinikov P, Shaytan A, Shi X, Studitsky V, Sokolova O
To Be Published
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Widom 603 dna sequence (44 kDa, DNA from synthetic construct)
- Widom 603 dna sequence (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Human nucleosome containing widom 603 dna sequence (Complex from Homo sapiens)
Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Histone h3.2 (Protein from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Dna (187-mer) (DNA from synthetic construct)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Protein from Homo sapiens)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Protein from Homo sapiens)
- Dna (187-mer) (Complex from synthetic construct)
- Overall map of ncprc1rybp bound to doubly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Ubiquitin (Protein from Homo sapiens)
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histones (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h1.4 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8vfx
Q-score: 0.559
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- 186bp albn1 nucleosome in complex with scfv (Complex from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (158-mer) (57 kDa, DNA from synthetic construct)
- Scfv (29 kDa, Protein from Mus musculus)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1)
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8vfy
Q-score: 0.463
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Foxa1 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2)
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8vfz
Q-score: 0.27
Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y
Mol Cell (2024) 84 pp. 3061- [ DOI: doi:10.1016/j.molcel.2024.07.016 Pubmed: 39121853 ]
- Foxa1 in complx with 186bp albn1 nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (171-mer) (57 kDa, DNA from synthetic construct)
- Hepatocyte nuclear factor 3-alpha (50 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)