Structure of C. thermophilum RNA exosome core
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8r1o
Q-score: 0.489
Liebau J, Lazzaretti D, Bichler A, Pilsl M, Sprangers R
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.28.577622 ]
- Rrp45 (32 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Putative exosome complex protein (38 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Rna exosome core (exo9) (294 kDa, Complex from Thermochaetoides thermophila DSM 1495)
- Exosome complex component mtr3 (30 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease phosphorolytic domain-containing protein (29 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease-like protein (39 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease phosphorolytic domain-containing protein (43 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Ribosomal rna-processing protein 40 (27 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Putative exosome 3'->5 protein (23 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease phosphorolytic domain-containing protein (27 kDa, Protein from Thermochaetoides thermophila DSM 1495)
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex bound to Spt4/5
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8oki
Q-score: 0.48
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex with spt4/5 (Complex)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8orq
Q-score: 0.477
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase open clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8p2i
Q-score: 0.461
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase open clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8rbo
Q-score: 0.246
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Pyrococcus furiosus apo form of rna polymerase contracted clamp conformation (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cryo-EM structure of Pyrococcus furiosus transcription elongation complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8cro
Q-score: 0.462
Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D
Nucleic Acids Res (2024) 52 pp. 6017-6035 [ Pubmed: 38709902 DOI: doi:10.1093/nar/gkae282 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex (tec) (Complex)
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (6 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna non-template strand (2 kDa, DNA from Pyrococcus furiosus DSM 3638)
Resolution: 4.09 Å
EM Method: Single-particle
Fitted PDBs: 8a43
Q-score: 0.337
Daiss JL, Pilsl M, Straub K, Bleckmann A, Hocherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars JC, Furtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C
Life Sci Alliance (2022) 5 [ Pubmed: 36271492 DOI: doi:10.26508/lsa.202201568 ]
- Dna-directed rna polymerase i subunit rpa2 (128 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa49 (47 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Rna polymerase i (Complex from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa1 (195 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa34 (55 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
Multibody refined monomer of the human NLRP3 decamer assembly.
Hochheiser IV, Pilsl M, Hagelueken G, Moecking J, Marleaux M, Brinkschulte R, Latz E, Engel C, Geyer M
Nature (2022) 604 pp. 184-189 [ Pubmed: 35114687 DOI: doi:10.1038/s41586-022-04467-w ]
- Decamer of human nlrp3 (1 MDa, Complex from Homo sapiens)
- Nlrp3 (Protein from Homo sapiens)
Focussed refinement of a NACHT domain of the human NLRP3 decamer.
Hochheiser IV, Pilsl M, Hagelueken G, Moecking J, Marleaux M, Brinkschulte R, Latz E, Engel C, Geyer M
Nature (2022) 604 pp. 184-189 [ Pubmed: 35114687 DOI: doi:10.1038/s41586-022-04467-w ]
- Decamer of human nlrp3 (1 MDa, Complex from Homo sapiens)
- Nlrp3 (Protein from Homo sapiens)
High resolution reconstruction of the human NLRP3 decamer
Hochheiser IV, Pilsl M, Hagelueken G, Moecking J, Marleaux M, Brinkschulte R, Latz E, Engel C, Geyer M
Nature (2022) 604 pp. 184-189 [ Pubmed: 35114687 DOI: doi:10.1038/s41586-022-04467-w ]
- Nlrp3 (Protein from Homo sapiens)
- Decamer of human nlrp3 (1 MDa, Complex from Homo sapiens)