Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9j0n
Q-score: 0.316
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*gp*up*gp*gp*up*gp*gp*cp*c)-3') (13 kDa, RNA from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0o
Q-score: 0.313
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9j0p
Q-score: 0.311
Naganuma M, Kujirai T, Ehara H, Uejima T, Ito T, Goto M, Aoki M, Henmi M, Miyamoto-Kohno S, Shirouzu M, Kurumizaka H, Sekine S
Sci Adv (2025) [ DOI: doi:10.1126/sciadv.adu0577 ]
- Rna (5'-r(p*ap*ap*up*up*ap*gp*cp*up*cp*up*up*gp*up*gp*up*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
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 [ Pubmed: 39196936 DOI: doi:10.1126/sciadv.adp0975 ]
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w9d
Q-score: 0.263
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 3-dna (45 kDa, DNA from Homo sapiens)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8w9e
Q-score: 0.188
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 3-dna (45 kDa, DNA from Homo sapiens)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8w9f
Q-score: 0.156
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 3-dna (45 kDa, DNA from Homo sapiens)
Structure of apo telomeric nucleosome
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 8ox0
Q-score: 0.607
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 [ Pubmed: 37624885 DOI: doi:10.1126/sciadv.adi4148 ]
- Histone h2b type 1-c/e/f/g/i (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Human telomeric nucleosome (Complex from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Trf1core in complex with telomeric nucleosome (Complex)
- Telomeric dna g strand (46 kDa, DNA from Homo sapiens)
- Telomeric dna c strand (43 kDa, DNA from Homo sapiens)
Structure of TRF1core in complex with telomeric nucleosome
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8ox1
Q-score: 0.579
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 repeat-binding factor 1 (50 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-c (14 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Human telomeric nucleosome (Complex from Homo sapiens)
- Human trf1core complex (Complex from Homo sapiens)
- Telomeric dna g strand (46 kDa, DNA from Homo sapiens)
- Telomeric repeat-binding factor 1 (50 kDa, Protein from Homo sapiens)
- Telomeric dna c strand (43 kDa, DNA from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (14 kDa, Protein from Homo sapiens)
- Trf1core in complex with telomeric nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8svf
Q-score: 0.383
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ DOI: doi:10.1126/sciadv.adg9832 Pubmed: 37556531 ]
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)