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 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a (Complex from Xenopus laevis)
- Histones octamer (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (314-mer) (Complex from synthetic construct)
- Histone h3.2 (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
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 ]
- Histone h3.2 (Complex from Xenopus laevis)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Cellular component from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ncprc1rybp bound to symmetric h2ak119ub dinucleosome (Complex from Homo sapiens)
- Ncprc1-rybp (Complex from Homo sapiens)
- Histone h4 (Complex from Xenopus laevis)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Histones octamer (Complex from Xenopus laevis)
- Dna (314-mer) (Complex from synthetic construct)
- Ubiquitin (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 [ DOI: doi:10.1016/j.molcel.2024.08.025 Pubmed: 39303719 ]
- Automethylated prc2 dimer bound to nucleosome (290 kDa, Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc finger protein aebp2 (34 kDa, Protein from Homo sapiens)
- Dna (226-mer) (66 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase ezh2 (86 kDa, Protein from Homo sapiens)
- Proximal prc2 (Complex from Homo sapiens)
- Distal prc2 (Complex from Homo sapiens)
- Polycomb protein eed (50 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- Dna (226-mer) (65 kDa, DNA from synthetic construct)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb protein suz12 (72 kDa, Protein from Homo sapiens)
- Activating methylated peptide (1 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a.z (13 kDa, Protein from Mus musculus)
- Chromobox protein homolog 5 (22 kDa, Protein from Homo sapiens)
- Hp1alpha dimer bound to h2a.z nucleosome (288 kDa, Complex from Escherichia coli)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna widom601 (208bp) strand2 (63 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna widom601 (208bp) strand1 (64 kDa, DNA from synthetic construct)
Class1 of the INO80-Hexasome complex
Resolution: 6.68 Å
EM Method: Single-particle
Fitted PDBs: 8ett
Q-score: 0.186
Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y
Science (2023) 381 pp. 319-324 [ DOI: doi:10.1126/science.adf4197 Pubmed: 37384669 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Class1 hexasome in ino80-hexasome complex (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (110-mer) (70 kDa, DNA from synthetic construct)
- Dna (110-mer) (69 kDa, DNA from synthetic construct)
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 7zsb
Q-score: 0.277
Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 226-232 [ Pubmed: 36411341 DOI: doi:10.1038/s41594-022-00865-w ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (38 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb4 (37 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iie subunit alpha (55 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Template dna (219-mer) (67 kDa, DNA from synthetic construct)
- Rna polymerase ii transcription factor b subunit 3 (38 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcription initiation factor iia subunit 2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcription initiation factor iie subunit beta (37 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb1 (73 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpd (89 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit tfb5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iia large subunit (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Tata-box-binding protein (28 kDa, Protein from Saccharomyces cerevisiae)
- Yeast rna polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (1 MDa, Complex from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Non-template dna (219-mer) (67 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih subunit ssl1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iib (39 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit alpha (82 kDa, Protein from Saccharomyces cerevisiae)
- General transcription and dna repair factor iih helicase subunit xpb (95 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb2 (138 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Transcription initiation factor iif subunit beta (46 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
The structure of SWI/SNF-nucleosome complex
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 7egp
Q-score: 0.105
He ZY, Chen KJ, Ye YP, Chen ZC
Cell Discov (2021) 7 pp. 28-28 [ DOI: doi:10.1038/s41421-021-00262-5 Pubmed: 33907182 ]
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf2 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Swi/snf complex subunit swi3 (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf6 (37 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- The structure of swi/snf chromatin remodeler complex (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf chromatin-remodeling complex subunit swi1 (124 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Swi/snf chromatin-remodeling complex subunit snf5 (103 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone (Complex from Xenopus laevis)
- Dna (239-mer) (72 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (239-mer) (72 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Swi/snf global transcription activator complex subunit swp82 (71 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcription regulatory protein snf12 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6w5i
Q-score: 0.135
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 6w5n
Q-score: 0.167
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Bilokapic S, Suskiewicz MJ, Ahel I, Halic M
Nature (2020) 585 pp. 609-613 [ DOI: doi:10.1038/s41586-020-2725-7 Pubmed: 32939087 ]
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from African clawed frog)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1, histone parylation factor 1, poly [adp-ribose] polymerase 2/dna complex (100 kDa, Complex)
- Dna (Complex from synthetic construct)
- Histone parylation factor 1, poly [adp-ribose] polymerase 2 (Complex from Homo sapiens)