RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egx
Q-score: 0.25
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egy
Q-score: 0.256
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9egz
Q-score: 0.261
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Rna (6 kDa, RNA from synthetic construct)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Template dna (66 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9eh0
Q-score: 0.24
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Template dna (61 kDa, DNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Non-template (60 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna (4 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eh1
Q-score: 0.237
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt6 (117 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (5 kDa, Protein from Sus scrofa)
- Histone h4 (8 kDa, Protein from Xenopus laevis)
- Rna polymerase-associated protein leo1 (14 kDa, Protein from Homo sapiens)
- Non-template dna (52 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (173 kDa, Protein from Sus scrofa)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (8 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (13 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt5 (57 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Superkiller complex protein 8, n-terminally processed (33 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (102 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Template dna (56 kDa, DNA from synthetic construct)
- Rna polymerase ii-associated factor 1 homolog (28 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (19 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Parafibromin (5 kDa, Protein from Homo sapiens)
- Rna (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone-lysine n-methyltransferase setd2 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (132 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Protein iws1 homolog (14 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rna polymerase rpb4/rpc9 core domain-containing protein (14 kDa, Protein from Sus scrofa)
RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9eh2
Q-score: 0.252
Markert JW, Soffers JH, Farnung L
Science (2025) 387 pp. 528-533 [ DOI: doi:10.1126/science.adn6319 Pubmed: 39666822 ]
- Protein iws1 homolog (92 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Rna polymerase-associated protein rtf1 homolog (80 kDa, Protein from Homo sapiens)
- Setd2 downstream complex (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from synthetic construct)
- Wdr61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt6 (199 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog (134 kDa, Protein from Homo sapiens)
- Fact complex subunit ssrp1 (81 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein leo1 (75 kDa, Protein from Homo sapiens)
- Non-template dna (63 kDa, DNA from synthetic construct)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase ii-associated factor 1 homolog (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Template dna (66 kDa, DNA from synthetic construct)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Fact complex subunit spt16 (120 kDa, Protein from Homo sapiens)
Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7y5u
Q-score: 0.345
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Chromatin assembly factor 1 subunit b (46 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- H3-h4 (Complex)
- Monomeric caf1l-h3-h4 complex (168 kDa, Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Chromatin assembly factor 1 subunit a (47 kDa, Protein from Homo sapiens)
- Caf1l/rbbp4/chromatin assembly factor 1 subunit b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex
Resolution: 6.1 Å
EM Method: Single-particle
Fitted PDBs: 7y5v
Q-score: 0.222
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Chromatin assembly factor 1 subunit b (46 kDa, Protein from Homo sapiens)
- Histone-binding protein rbbp4 (47 kDa, Protein from Homo sapiens)
- H3-h4 (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Chromatin assembly factor 1 subunit a (47 kDa, Protein from Homo sapiens)
- Caf1lc/rbbp4 (Complex from Homo sapiens)
- Dimeric caf1lc-h3-h4 complex (336 kDa, Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Cryo-EM structure of the left-handed Di-tetrasome
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7y5w
Q-score: 0.35
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Dna (Complex)
- H3-h4 (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- A left-handed di-tetrasome (Complex from Homo sapiens)
Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7y60
Q-score: 0.304
Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM
Science (2023) 381 pp. eadd8673-eadd8673 [ Pubmed: 37616371 DOI: doi:10.1126/science.add8673 ]
- Chromatin assembly factor 1 subunit b (46 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)
- Chromatin assembly factor 1 subunit a (47 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- The caf1lc bound right-handed di-tetrasome (Complex from Homo sapiens)
- Widom 601 dna (147-mer) (45 kDa, DNA from synthetic construct)