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) [ Pubmed: 39762629 DOI: doi:10.1038/s41594-024-01448-7 ]
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit (217 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 ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- 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 rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii bound to alu rna right arm (48 kDa, Complex)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Alu rna right arm (Complex 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 rpabc5 (7 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) [ Pubmed: 39762629 DOI: doi:10.1038/s41594-024-01448-7 ]
- Dna-directed rna polymerase ii subunit polr2j (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2i (Protein from Sus scrofa domesticus)
- Alu rna left arm (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2c (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2h (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2k (Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2f (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2l (Protein from Sus scrofa domesticus)
- Alu rna left arm (RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2d (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2g (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)
- Dna-directed rna polymerase ii subunit polr2e (Protein from Sus scrofa domesticus)
- Rna polymerase ii bound to alu rna left arm (36 kDa, Complex)
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 polr2a (Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2d (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2h (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2j (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2k (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2g (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2f (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2l (Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit polr2b (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2i (Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (Complex from Homo sapiens)
- Rna polymerase ii bound to minimal alu rna right arm in the canonical conformation (24 kDa, Complex)
- Dna-directed rna polymerase ii subunit polr2e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit polr2c (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 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii, i and iii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii bound to alu rna minimal right arm (24 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 (217 kDa, Protein from Sus scrofa domesticus)
- Alu rna minimal right arm (Complex from Homo sapiens)
- 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)
Structure of Sen1 bound RNA Polymerase II pre-termination complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ram
Q-score: 0.394
Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01409-0 Pubmed: 39424994 ]
- Transcription elongation factor 1 (16 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 rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Rna polymerase ii (Complex from Saccharomyces cerevisiae)
- Template strand (18 kDa, DNA from Human immunodeficiency virus 2)
- Sen1 bound rna polymerase ii pre-termination complex (Complex)
- Transcription elongation factors (Complex from Saccharomyces cerevisiae)
- Non-template strand (17 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Rna (11 kDa, RNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Helicase sen1 (252 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Dna and rna (Complex from Human immunodeficiency virus 2)
- Magnesium ion (24 Da, Ligand)
Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8rap
Q-score: 0.24
Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P
Nat Struct Mol Biol (2024) [ DOI: doi:10.1038/s41594-024-01409-0 Pubmed: 39424994 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Saccharomyces cerevisiae)
- Beryllium trifluoride ion (66 Da, Ligand)
- Rna (11 kDa, RNA from Human immunodeficiency virus 2)
- Tertiary complex of rna polymerase ii with elongation factors elf1, spt4, spt5 and the termination factor sen1 (Complex)
- Dna-directed rna polymerase ii subunit rpb3 (35 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii (Complex from Saccharomyces cerevisiae)
- Non-template strand (17 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (17 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor spt5 (115 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factor 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb11 (13 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Template strand (18 kDa, DNA from Human immunodeficiency virus 2)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex from Human immunodeficiency virus 2)
- Rna (Complex from Human immunodeficiency virus 2)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb1 (191 kDa, Protein from Saccharomyces cerevisiae)
- Transcription elongation factors (Complex from Saccharomyces cerevisiae)
- Helicase sen1 (252 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 elongation factor spt4 (11 kDa, Protein from Saccharomyces cerevisiae)
- Dna-directed rna polymerase ii subunit rpb4 (25 kDa, Protein from Saccharomyces cerevisiae)
Structure of the mammalian Pol II-SPT6 complex, Struture 4 (Global map)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- The pol ii-spt6 transcription elongation complex (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (Protein from Sus scrofa)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- Transcription elongation factor spt6 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Rpb3 (Protein from Sus scrofa)
- Rpb9 (Protein from Sus scrofa)
- Non-template dna (DNA from synthetic construct)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Spt6h (Protein from Homo sapiens)
- Eloa1 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Eloc (Protein from Homo sapiens)
- Rpb6 (Protein from Sus scrofa)
- Rpb1 (Protein from Sus scrofa)
- Rpb4 (Protein from Sus scrofa)
- Rpb5 (Protein from Sus scrofa)
- Rpb8 (Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rpb2 (Protein from Sus scrofa)
- Template dna (DNA from synthetic construct)
- Elob (Protein from Homo sapiens)
- Rpb7 (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]
- Template dna (DNA from synthetic construct)
- Elongin b (Protein from Homo sapiens)
- Elongin a (Protein from Homo sapiens)
- Non-template dna (DNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa)
- Rna polymerase ii subunit k (Protein from Sus scrofa)
- Rna polymerase ii subunit f (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa)
- Rna polymerase ii subunit e (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa)
- Rna (RNA from synthetic construct)
- Transcription elongation factor spt6 (Protein from Homo sapiens)
- Elongin c (Protein from Homo sapiens)
- Rna polymerase ii subunit d (Protein from Sus scrofa)
- The pol ii-spt6-elongin transcription elongation complex (Complex from Homo sapiens)
- Rna polymerase ii subunit rpb9 (Protein from Sus scrofa)
- Rna polymerase ii subunit g (Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa)
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
Nat Struct Mol Biol (2023) 30 pp. 1925-1935 [ Pubmed: 37932450 DOI: doi:10.1038/s41594-023-01138-w ]