RNA polymerase II bound to Alu RNA right arm
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8qep
Q-score: 0.55
Tluckova K, Kaczmarek B, Salmazo A, Bernecky C
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01448-7 Pubmed: 39762629 ]
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii bound to alu rna right arm (48 kDa, Complex)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Alu rna right arm (Complex from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
RNA polymerase II bound to Alu RNA left arm
Tluckova K, Kaczmarek B, Salmazo A, Bernecky C
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01448-7 Pubmed: 39762629 ]
- Rna polymerase ii bound to alu rna left arm (36 kDa, Complex)
- Dna-directed rna polymerase ii subunit polr2d (Protein from Sus scrofa domesticus)
- Alu rna left arm (RNA from Homo sapiens)
- Alu rna left arm (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2k (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2c (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2g (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2h (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2i (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2b (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2f (Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2l (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2j (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2a (Protein from Sus scrofa domesticus)
RNA polymerase II bound to minimal Alu RNA right arm in the canonical conformation
Tluckova K, Kaczmarek B, Salmazo A, Bernecky C
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01448-7 Pubmed: 39762629 ]
- Dna-directed rna polymerase ii subunit polr2d (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2k (Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2c (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2g (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2h (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2i (Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2e (Protein from Sus scrofa domesticus)
- Rna polymerase ii bound to minimal alu rna right arm in the canonical conformation (24 kDa, Complex)
- Dna-directed rna polymerase ii subunit polr2f (Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2l (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2j (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2b (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2a (Protein from Sus scrofa domesticus)
RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qeq
Q-score: 0.523
Tluckova K, Kaczmarek B, Salmazo A, Bernecky C
Nat Struct Mol Biol (2025) [ DOI: doi:10.1038/s41594-024-01448-7 Pubmed: 39762629 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (24 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii bound to alu rna minimal right arm (24 kDa, Complex)
Structure of Pol II-TC-NER-STK19 complex, consensus map
Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA
Mol Cell (2024) 84 pp. 4740-4757.e12 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, consensus map (1 MDa, Complex from Homo sapiens)
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Nedd8 (Protein from Homo sapiens)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Cullin-4a (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
Structure of Pol II-TC-NER-STK19 complex, focused on Pol II-ELOF1
Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA
Mol Cell (2024) 84 pp. 4740-4757.e12 [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, focused on pol ii-elof1 (550 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
Structure of Pol II-TC-NER-STK19 complex, composite map
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9fd2
Q-score: 0.436
Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA
Mol Cell (2024) 84 pp. 4740- [ Pubmed: 39547223 DOI: doi:10.1016/j.molcel.2024.10.030 ]
- Det1- and ddb1-associated protein 1 (16 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Template dna (18 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Rna (8 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (18 kDa, DNA from Homo sapiens)
- Uv-stimulated scaffold protein a (82 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Ternary complex of pol ii-tc-ner-stk19, composite map (1 MDa, Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC3
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5oik
Q-score: 0.373
Bernecky C, Plitzko JM, Cramer P
Nat Struct Mol Biol (2017) 24 pp. 809-815 [ Pubmed: 28892040 DOI: doi:10.1038/nsmb.3465 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Bos taurus)
- Uncharacterized protein (17 kDa, Protein from Bos taurus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Bos taurus)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Bos taurus)
- Polymerase (rna) ii (dna directed) polypeptide d (16 kDa, Protein from Bos taurus)
- Rna polymerase ii-dsif elongation complex (690 kDa, Complex)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-rna synthetic construct (40 kDa, Complex from synthetic construct)
- Rna (5'-r(p*up*ap*up*ap*up*ap*cp*ap*up*ap*ap*ap*gp*ap*cp*cp*ap*gp*gp*c)-3') (16 kDa, RNA from synthetic construct)
- Rna polymerase ii (520 kDa, Complex from Bos taurus)
- Magnesium ion (24 Da, Ligand)
- Dsif (130 kDa, Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Bos taurus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Bos taurus)
- Dna (43-mer) (13 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Bos taurus)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Bos taurus)
Structure of transcribing mammalian RNA polymerase II (EC1)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5flm
Q-score: 0.442
Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P
Nature (2016) 529 pp. 551-554 [ DOI: doi:10.1038/nature16482 Pubmed: 26789250 ]
- Dna-directed rna polymerase ii (520 kDa, Protein from Bos taurus)
- Bovine pol ii elongation complex (590 kDa, Sample)
- Dna-rna synthetic construct (30 kDa, Macromolecule from unidentified)
- Dna-directed rna polymerase ii subunit grinl1a (40 kDa, Protein from Homo sapiens)
Molecular architecture of the human VP16-Mediator-RNA polymerase II-TFIIF assembly
Resolution: 36.0 Å
EM Method: Single-particle
Fitted PDBs: 3j0k
Q-score: 0.026
Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ
PLoS Biol (2011) 9 pp. e1000603-e1000603 [ Pubmed: 21468301 DOI: doi:10.1371/journal.pbio.1000603 ]
- Core mediator (1 MDa, Protein from Homo sapiens)
- Rna polymerase ii (520 kDa, Protein from Homo sapiens)
- Assembly of vp16-bound human mediator, rna polymerase ii, and tfiif (1 MDa, Sample)
- Tfiif (10 kDa, Protein from Homo sapiens)