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 f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 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)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
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 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- 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 subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
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 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase ii (Complex from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Histone proteins (Complex from Homo sapiens)
- 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 subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
human co-transcriptional RNA capping enzyme RNGTT
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w8e
Q-score: 0.265
Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Human co-transcriptional rna capping enzyme rngtt (Complex)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor, transcription elongation factor, mrna-capping enzyme (Complex from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polimerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (65 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Negative elongation factor e (43 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna,rna (Complex from Homo sapiens)
- Rna (5'-d(*(gtp))-r(p*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
human co-transcriptional RNA capping enzyme RNGTT-CMTR1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8w8f
Q-score: 0.228
Nat Commun (2024) 15 pp. 4622-4622 [ Pubmed: 38816438 DOI: doi:10.1038/s41467-024-48963-1 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 (95 kDa, Protein from Homo sapiens)
- Human co-transcriptional rna capping enzyme rngtt-cmtr1 (Complex)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Rna (5'-r(p*gp*ap*gp*ap*gp*ap*gp*gp*gp*ap*ap*cp*cp*cp*ap*cp*u)-3') (5 kDa, RNA from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Dna (45-mer) (14 kDa, DNA from Homo sapiens)
- Dna-rna (Complex from Homo sapiens)
- Dna-directed rna polymerase (Complex from Sus scrofa)
- Transcription elongation factor, m-rna capping enzyme, cmtr1 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna (36-mer) (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Mrna-capping enzyme (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
Resolution: 5.47 Å
EM Method: Single-particle
Fitted PDBs: 8wak
Q-score: 0.079
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Alpha-amanitin (Complex from Amanita phalloides)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Structure of transcribing complex 2 (tc2), the initially transcribing complex with pol ii positioned 2nt downstream of tss (Complex)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna (847 Da, RNA from synthetic construct)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (Complex from synthetic construct)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Tfiih (Complex from Homo sapiens)
Resolution: 8.52 Å
EM Method: Single-particle
Fitted PDBs: 8wal
Q-score: 0.084
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Alpha-amanitin (Complex from Amanita phalloides)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Structure of transcribing complex 3 (tc3), the initially transcribing complex with pol ii positioned 3nt downstream of tss (Complex)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Rna (1 kDa, RNA from synthetic construct)
- Tfiie (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Template dna (30 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (Complex from synthetic construct)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Tfiih (Complex from Homo sapiens)
Resolution: 6.07 Å
EM Method: Single-particle
Fitted PDBs: 8wan
Q-score: 0.078
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Rna (1 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Alpha-amanitin (Complex from Amanita phalloides)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Template dna (30 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- Structure of transcribing complex 4 (tc4), the initially transcribing complex with pol ii positioned 4nt downstream of tss (Complex)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (Complex from synthetic construct)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Tfiih (Complex from Homo sapiens)
Resolution: 6.4 Å
EM Method: Single-particle
Fitted PDBs: 8wao
Q-score: 0.075
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Alpha-amanitin (Complex from Amanita phalloides)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna (1 kDa, RNA from synthetic construct)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Structure of transcribing complex 5 (tc5), the initially transcribing complex with pol ii positioned 5nt downstream of tss (Complex)
- Zinc ion (65 Da, Ligand)
- Template dna (30 kDa, DNA from synthetic construct)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (Complex from synthetic construct)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Tfiih (Complex from Homo sapiens)
Resolution: 5.85 Å
EM Method: Single-particle
Fitted PDBs: 8wap
Q-score: 0.081
Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y
Science (2023) 382 pp. eadi5120-eadi5120 [ Pubmed: 38127763 DOI: doi:10.1126/science.adi5120 ]
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpd (87 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 1 (58 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 4 (52 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 6 (72 kDa, Protein from Homo sapiens)
- Transcription initiation factor iib (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Alpha-amanitin (Complex from Amanita phalloides)
- Tfiia (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 7 (40 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 3 (103 kDa, Protein from Homo sapiens)
- Structure of transcribing complex 6 (tc6), the initially transcribing complex with pol ii positioned 6nt downstream of tss (Complex)
- Tata-box-binding protein (37 kDa, Protein from Homo sapiens)
- Template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 11 (23 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 13 (14 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 5 (86 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia beta chain (41 kDa, Protein from Homo sapiens)
- Rna (Complex from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Transcription initiation factor tfiid subunit 9 (29 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Transcription initiation factor tfiid subunit 1 (212 kDa, Protein from Homo sapiens)
- General transcription factor iif subunit 2 (28 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- General transcription and dna repair factor iih helicase subunit xpb (89 kDa, Protein from Homo sapiens)
- Non-template dna (30 kDa, DNA from synthetic construct)
- Transcription initiation factor tfiid subunit 8 (34 kDa, Protein from Homo sapiens)
- Tfiib (Complex from Homo sapiens)
- Alpha-amanitin (939 Da, Protein from Amanita phalloides)
- General transcription factor iie subunit 1 (49 kDa, Protein from Homo sapiens)
- [[(2~{s},3~{r},4~{s},5~{r})-5-(2-azanyl-6-oxidanylidene-3~{h}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (537 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rna (2 kDa, RNA from synthetic construct)
- Transcription initiation factor tfiid subunit 4 (110 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 5 (8 kDa, Protein from Homo sapiens)
- Cdk-activating kinase assembly factor mat1 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Transcription initiation factor tfiid subunit 12 (17 kDa, Protein from Homo sapiens)
- Transcription initiation factor iia subunit 2 (12 kDa, Protein from Homo sapiens)
- Tfiie (Complex from Homo sapiens)
- Tfiid (Complex from Homo sapiens)
- Transcription initiation factor tfiid subunit 10 (21 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 3 (34 kDa, Protein from Homo sapiens)
- Transcription initiation factor iie subunit beta (33 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- General transcription factor iih subunit 2 (44 kDa, Protein from Homo sapiens)
- Transcription initiation factor tfiid subunit 2 (137 kDa, Protein from Homo sapiens)
- General transcription factor iih subunit 1 (62 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna (Complex from synthetic construct)
- Tfiif (Complex from Homo sapiens)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Tfiih (Complex from Homo sapiens)