The structural basis for RNA slicing by human Argonatue2 (Map 1)
Mohamed AA, Wang PY, Bartel DP, Vos SM
Cell Rep (2025) 44 pp. 115166-115166 [ DOI: doi:10.1016/j.celrep.2024.115166 Pubmed: 39932188 ]
- Mir7-hsago2 risc (113 kDa, Complex from Homo sapiens)
Structure of human Argonaute2-guide-target complex in a fully paired, slicing-competent conformation
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9cmp
Q-score: 0.301
Mohamed AA, Wang PY, Bartel DP, Vos SM
Cell Rep (2025) 44 pp. 115166-115166 [ DOI: doi:10.1016/j.celrep.2024.115166 Pubmed: 39932188 ]
- Protein argonaute-2 (97 kDa, Protein from Homo sapiens)
- Mir7-hsago2 risc (113 kDa, Complex from Homo sapiens)
- Rna (5'-r(p*up*gp*gp*ap*ap*gp*ap*cp*up*ap*gp*up*gp*ap*up*up*up*up*gp*up*u)-3') (7 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(*cp*ap*ap*cp*ap*ap*ap*ap*up*cp*ap*cp*up*ap*gp*up*cp*up*up*cp*cp*a)-3') (8 kDa, RNA from Homo sapiens)
Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8a3y
Q-score: 0.231
Farnung L, Ochmann M, Garg G, Vos SM, Cramer P
Mol Cell (2022) 82 pp. 3126-3134.e7 [ Pubmed: 35858621 DOI: doi:10.1016/j.molcel.2022.06.027 ]
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Wd repeat-containing protein 61 (33 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna, template dna (9 kDa, RNA from synthetic construct)
- Non-template dna (39 kDa, DNA from synthetic construct)
- Rna polymerase ii-associated factor 1 homolog (36 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Spt6 (117 kDa, Protein from Homo sapiens)
- Rna polymerase-associated protein rtf1 homolog (29 kDa, Protein from Homo sapiens)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna, template dna (42 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (142 kDa, Protein from Sus scrofa)
- Mammalian pol ii-tfiis elongation complex (Complex from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (219 kDa, Protein from Sus scrofa)
- Parafibromin (60 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna polymerase-associated protein ctr9 homolog,rna polymerase-associated protein leo1 (210 kDa, Protein from Homo sapiens)
Structure of activated elongation complex with hexasome (Pol II focused)
Structure of paused transcription complex Pol II-DSIF-NELF - tilted
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8uha
Q-score: 0.28
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna (38-mer) (15 kDa, DNA from synthetic construct)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 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)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna (28-mer) (15 kDa, DNA from synthetic construct)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 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 in complex with dsif and nelf (Complex)
- Rna (5 kDa, RNA from synthetic construct)
- 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-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8uhd
Q-score: 0.353
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Transcription elongation factor spt4 (13 kDa, Protein from Homo sapiens)
- Negative elongation factor a (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Negative elongation factor b (65 kDa, Protein from Homo sapiens)
- Rna polymerase ii subunit j (13 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)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Template dna (15 kDa, DNA from synthetic construct)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase in complex with dsif and nelf (Complex)
- 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-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Structure of paused transcription complex Pol II-DSIF-NELF - poised post-translocated
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8uhg
Q-score: 0.353
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Template dna (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- 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-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Structure of poised transcription complex Pol II-DSIF-NELF - pre-translocated
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8ui0
Q-score: 0.352
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Rna polymerase in complex with dsif and nelf (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna (15 kDa, DNA from synthetic construct)
- Negative elongation factor a (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Dna (38-mer) (11 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Negative elongation factor b (63 kDa, Protein from Homo sapiens)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Rna (5 kDa, RNA from synthetic construct)
- 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-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
Structure of transcription complex Pol II-DSIF-NELF-TFIIS
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 8uis
Q-score: 0.319
Mol Cell (2024) 84 pp. 1243- [ DOI: doi:10.1016/j.molcel.2024.01.023 Pubmed: 38401543 ]
- Transcription elongation factor spt5 (121 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Negative elongation factor a (57 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit j (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Transcription elongation factor a protein 1 (34 kDa, Protein from Homo sapiens)
- Negative elongation factor c/d (66 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Rna polymerase in complex with dsif, nelf, tfiis (Complex)
- Template dna (15 kDa, DNA from synthetic construct)
- Rna polymerase rpb4/rpc9 core domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
- Rna (6 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase ii subunit rpb3 (30 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Non-template dna (15 kDa, DNA from synthetic construct)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)