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 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 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (Protein from Sus scrofa domesticus)
- E3 ubiquitin-protein ligase rbx1 (Protein from Homo sapiens)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Dna excision repair protein ercc-6 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Cullin-4a (Protein from Homo sapiens)
- Ternary complex of pol ii-tc-ner-stk19, consensus map (1 MDa, Complex from Homo sapiens)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (Protein from Sus scrofa domesticus)
- Inactive serine/threonine-protein kinase 19 (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (Protein from Sus scrofa domesticus)
- Nedd8 (Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
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 [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (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 rpb3 (Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (Protein from Homo sapiens)
- Non-template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb9 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit rpb7 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb11-a (Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (Protein from Sus scrofa domesticus)
- Template strand dna (DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb1 (Protein from Sus scrofa domesticus)
- Rna (RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (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- [ DOI: doi:10.1016/j.molcel.2024.10.030 Pubmed: 39547223 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Template dna (18 kDa, DNA 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 (217 kDa, Protein from Sus scrofa domesticus)
- Zinc ion (65 Da, Ligand)
- Uv-stimulated scaffold protein a (82 kDa, Protein from Homo sapiens)
- Rna polymerase ii, i and iii subunit k (7 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 rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (16 kDa, Protein from Homo sapiens)
- 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)
- Dna-directed rna polymerase subunit beta (147 kDa, Protein from Sus scrofa domesticus)
- Ternary complex of pol ii-tc-ner-stk19, composite map (1 MDa, Complex from Homo sapiens)
- Non-template dna (18 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Rna (8 kDa, RNA from Homo sapiens)
- Dna excision repair protein ercc-8 (45 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
Structure of the Pol II-TCR-ELOF1 complex.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b3d
Q-score: 0.532
To Be Published
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Rna (3 kDa, RNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 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 polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Nts (16 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Pol ii-tcr-elof1 complex. (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rpb7 (28 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b3f
Q-score: 0.456
To Be Published
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Pol ii-csb-csa-ddb1-elof1 complex. (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna (3 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Nts (16 kDa, DNA from Homo sapiens)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Magnesium ion (24 Da, Ligand)
- Dna excision repair protein ercc-8 (44 kDa, Protein 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)
Structural basis of Integrator-mediated transcription regulation
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7pks
Q-score: 0.278
Fianu I, Chen Y, Dienemann C, Dybkov O, Linden A, Urlaub H, Cramer P
Science (2021) 374 pp. 883-887 [ DOI: doi:10.1126/science.abk0154 Pubmed: 34762484 ]
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor e (1 kDa, Protein from Homo sapiens)
- Pol ii-ec (Complex from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (14 kDa, DNA from Human immunodeficiency virus 1)
- Integrator complex subunit 11 (67 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 1 (244 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Human integrator-pp2a complex (Complex from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Unknown (2 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Template dna (Complex from Human immunodeficiency virus 1)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Non-template dna (Complex from Human immunodeficiency virus 1)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 6 (100 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Integrator complex subunit 9 (73 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Rna (Complex from Human immunodeficiency virus 1)
- Integrator complex subunit 2 (134 kDa, Protein from Homo sapiens)
- Integrator complex subunit 8 (113 kDa, Protein from Homo sapiens)
- Rpbi c-terminal domain peptide (1 kDa, Protein from Sus scrofa domesticus)
- Manganese (ii) ion (54 Da, Ligand)
- Integrator complex subunit 5 (108 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Negative elongation factor b (68 kDa, Protein from Homo sapiens)
- Integrator complex subunit 4 (108 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a catalytic subunit alpha isoform (35 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Pec-integrator-pp2a complex (1 MDa, Complex)
- Dna template (14 kDa, DNA from Human immunodeficiency virus 1)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dsif (Complex from Homo sapiens)
- Integrator complex subunit 7 (106 kDa, Protein from Homo sapiens)
- Tar rna (5 kDa, RNA from Human immunodeficiency virus 1)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
- Serine/threonine-protein phosphatase 2a 65 kda regulatory subunit a alpha isoform (65 kDa, Protein from Homo sapiens)
- Nelf (Complex from Homo sapiens)