structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome
Resolution: 3.34 Å
EM Method: Single-particle
Fitted PDBs: 8cbn
Q-score: 0.392
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Dna (Complex from Homo sapiens)
- H3k36me3 dinucleosome-ledgf/p75 pwwp domain complex (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Histone (Complex from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ledgf/p75 pwwp domain protein (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (50 kDa, DNA from synthetic construct)
structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8cbq
Q-score: 0.304
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Dna (Complex from Homo sapiens)
- Ledgf/p75 pwwp domain complex (Complex)
- H3k36me3 dinucleosome-ledgf/p75 pwwp domain complex (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Histone (Complex from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (50 kDa, DNA from synthetic construct)
H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8pc5
Q-score: 0.521
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- H3k36me3 nucleosome-ledgf/p75 pwwp domain complex (Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8pc6
Q-score: 0.484
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- H3k36me3 nucleosome-ledgf/p75 pwwp domain complex - pose 2 (Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8peo
Q-score: 0.548
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- H3k36me2 nucleosome-ledgf/p75 pwwp domain complex (Complex from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8pep
Q-score: 0.399
Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V
Nucleic Acids Res (2023) 51 pp. 10011-10025 [ DOI: doi:10.1093/nar/gkad674 Pubmed: 37615563 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pc4 and sfrs1-interacting protein (60 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- H3k36me2 nucleosome-ledgf/p75 pwwp domain complex - pose 2 (Complex from Xenopus laevis)
PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6wkr
Q-score: 0.362
Kasinath V, Beck C, Sauer P, Poepsel S, Kosmatka J, Faini M, Toso D, Aebersold R, Nogales E
Science (2021) 371 [ DOI: doi:10.1126/science.abc3393 Pubmed: 33479123 ]
- Protein jumonji (49 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Prc2-aebp2-jarid2 bound to h2ak119ub1 nucleosome (500 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase ezh2 (85 kDa, Protein from Homo sapiens)
- Zinc finger protein aebp2 (33 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2ak119ub1 nucleosome (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Prc2-aebp2-jarid2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (314-mer) (98 kDa, DNA from Homo sapiens)
Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2.
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 7at8
Q-score: 0.29
Finogenova K, Bonnet J, Poepsel S, Schafer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Muller J
eLife (2020) 9 [ Pubmed: 33211010 DOI: doi:10.7554/eLife.61964 ]
- Widom601 dna plus linker (48 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Suz12 and ezh2 (Complex from Homo sapiens)
- Widom601 dna plus linker (47 kDa, DNA from synthetic construct)
- Em map of ezh2 on nucleosome obtained from signal particle subtraction and focused refinement on phf1-prc2:dinucleosome map. (Complex)
- Polycomb protein suz12 (83 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Isoform 2 of histone-lysine n-methyltransferase ezh2,isoform 2 of histone-lysine n-methyltransferase ezh2,histone-lysine n-methyltransferase ezh2,isoform 2 of histone-lysine n-methyltransferase ezh2,isoform 2 of histone-lysine n-methyltransferase ezh2 (87 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome.
Finogenova K, Bonnet J, Poepsel S, Schafer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Muller J
eLife (2020) 9 [ Pubmed: 33211010 DOI: doi:10.7554/eLife.61964 ]
- Polycomb protein suz12 (Protein from Homo sapiens)
- Widom601 dna + linker (Complex from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Polycomb protein eed (Protein from Homo sapiens)
- Histone h4 (Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase ezh2 (Protein from Homo sapiens)
- Histone h2b (Protein from Xenopus laevis)
- Widom601 dna + linker (RNA from synthetic construct)
- Histone h2a (Protein from Xenopus laevis)
- Cryo-em map of phf1-prc2 on a heterodimeric dinucleosome (Complex)
- Histone-lysine n-methyltransferase ezh2, polycomb protein eed, polycomb protein suz12 (Complex from Homo sapiens)
- Histone h3.2 (Protein from Xenopus laevis)