ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
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 ]
- Zinc ion (65 Da, Ligand)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
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 ]
- Zinc ion (65 Da, Ligand)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- 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)
Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C
Sci Adv (2024) 10 pp. eadp0975-eadp0975 [ DOI: doi:10.1126/sciadv.adp0975 Pubmed: 39196936 ]
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8t9f
Q-score: 0.516
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell (2023) 83 pp. 2872-2883.e7 [ DOI: doi:10.1016/j.molcel.2023.07.020 Pubmed: 37595555 ]
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Dna (122-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase kmt5b (44 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Suv420h1-h2a.z nucleosome complex (Complex from Xenopus laevis)
The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7vdt
Q-score: 0.549
Yuan JJ, Chen KJ, Zhang WB, Chen ZC
Nature (2022) 605 pp. 166-171 [ DOI: doi:10.1038/s41586-022-04658-5 Pubmed: 35477757 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (207-mer) (64 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- The motor-nucleosome module of human chromatin remodeling pbaf-nucleosome complex (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (207-mer) (63 kDa, DNA from synthetic construct)
- Isoform 2 of transcription activator brg1 (169 kDa, Protein from Homo sapiens)
The structure of ALC1 bound to the nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7enn
Q-score: 0.567
Nat Commun (2021) 12 pp. 4057-4057 [ Pubmed: 34210977 DOI: doi:10.1038/s41467-021-24320-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Histone (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Alc1 (Complex from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- The structure of alc1 bound to the nucleosome (Complex)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (101 kDa, Protein from Homo sapiens)