Overall structure of the U11 snRNP
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8r7n
Q-score: 0.306
Zhao J, Peter D, Brandina I, Liu X, Galej WP
Mol Cell (2025) 85 pp. 652- [ Pubmed: 39809272 DOI: doi:10.1016/j.molcel.2024.12.017 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 48 kda protein (40 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 35 kda protein (29 kDa, Protein from Homo sapiens)
- Zinc finger matrin-type protein 5 (20 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 25 kda protein (15 kDa, Protein from Homo sapiens)
- Overall structure of the apo-u11 snrnp (300 kDa, Complex from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Programmed cell death protein 7 (54 kDa, Protein from Homo sapiens)
- U11 snrna (43 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
TAS2R14 receptor bound to flufenamic acid and gustducin
Peri L, Matzov D, Huxley DR, Rainish A, Fierro F, Sapir L, Pfeiffer T, Waterloo L, Hubner H, Peleg Y, Gmeiner P, McCormick PJ, Weikert D, Niv MY, Shalev-Benami M
Nat Commun (2024) 15 pp. 9991-9991 [ DOI: doi:10.1038/s41467-024-54157-6 Pubmed: 39557861 ]
Overall structure of the substrate-bound U11 snRNP
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9gbw
Q-score: 0.32
Zhao J, Peter D, Brandina I, Liu X, Galej WP
Mol Cell (2025) 85 pp. 652- [ Pubmed: 39809272 DOI: doi:10.1016/j.molcel.2024.12.017 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 48 kda protein (40 kDa, Protein from Homo sapiens)
- Overall structure of the substrate-bound u11 snrnp (400 kDa, Complex from Homo sapiens)
- P120-5'ss (3 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 35 kda protein (29 kDa, Protein from Homo sapiens)
- Zinc finger matrin-type protein 5 (20 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 25 kda protein (15 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Programmed cell death protein 7 (54 kDa, Protein from Homo sapiens)
- U11 snrna (43 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
3'-lobe of the substrate-bound U11 snRNP
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9gc0
Q-score: 0.393
Zhao J, Peter D, Brandina I, Liu X, Galej WP
Mol Cell (2025) 85 pp. 652- [ Pubmed: 39809272 DOI: doi:10.1016/j.molcel.2024.12.017 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 48 kda protein (40 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Zinc finger matrin-type protein 5 (20 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Programmed cell death protein 7 (54 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- 3'-lobe of the substrate-bound u11 snrnp (300 kDa, Complex from Homo sapiens)
- U11 snrna (43 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
Structure of the U11 snRNP C-lobe
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9gcl
Q-score: 0.413
Zhao J, Peter D, Brandina I, Liu X, Galej WP
Mol Cell (2025) 85 pp. 652- [ Pubmed: 39809272 DOI: doi:10.1016/j.molcel.2024.12.017 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- U11 snrna (43 kDa, RNA from Homo sapiens)
- U11/u12 small nuclear ribonucleoprotein 48 kda protein (40 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Zinc finger matrin-type protein 5 (20 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Structure of the apo-u11 snrnp 3-lobe (300 kDa, Complex from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
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 ]
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex 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)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Template dna (168-mer) (60 kDa, DNA from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Non-template dna (157-mer) (61 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
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 ]
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- 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)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
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 ]
- Negative elongation factor c/d (68 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Rna polymerase ii in complex with dsif, nelf, and nucleosome (Complex)
- 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)
- Transcription elongation factor spt5 (123 kDa, Protein from Homo sapiens)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Rna polymerase ii (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rpb12 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Histone proteins (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Spt4 and spt5 (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Negative elongation factor (nelf) (Complex from Homo sapiens)
- Negative elongation factor e (45 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Non-template dna (180-mer) (61 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Template dna (191-mer) (60 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb4 (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 9cr2
Q-score: 0.162
QRB DISCOV (2024) [ DOI: doi:10.1017/qrd.2024.17 ]
- Tric subunit gamma (Complex from Saccharomyces cerevisiae)
- T-complex protein 1 subunit epsilon (61 kDa, Protein from Saccharomyces cerevisiae)
- T-complex protein 1 subunit eta (59 kDa, Protein from Saccharomyces cerevisiae)
- Tric at adp state1 (960 kDa, Complex)
- T-complex protein 1 subunit gamma (65 kDa, Protein from Saccharomyces cerevisiae)
- T-complex protein 1 subunit alpha (60 kDa, Protein from Saccharomyces cerevisiae)
- T-complex protein 1 subunit theta (61 kDa, Protein from Saccharomyces cerevisiae)
- Other tric proteins (Complex from Saccharomyces cerevisiae)
- T-complex protein 1 subunit zeta (59 kDa, Protein from Saccharomyces cerevisiae)
- T-complex protein 1 subunit beta (57 kDa, Protein from Saccharomyces cerevisiae)
- T-complex protein 1 subunit delta (57 kDa, Protein from Saccharomyces cerevisiae)
TAS2R14 receptor bound to flufenamic acid and gustducin
Peri L, Matzov D, Huxley DR, Rainish A, Fierro F, Sapir L, Pfeiffer T, Waterloo L, Hubner H, Peleg Y, Gmeiner P, McCormick PJ, Weikert D, Niv MY, Shalev-Benami M
Nat Commun (2024) 15 pp. 9991-9991 [ DOI: doi:10.1038/s41467-024-54157-6 Pubmed: 39557861 ]