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 ]
- Exosome complex component mtr3 (30 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Putative exosome complex protein (38 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease-like protein (39 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Exoribonuclease phosphorolytic domain-containing protein (29 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Putative exosome 3'->5 protein (23 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Rrp45 (32 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)
- Exoribonuclease phosphorolytic domain-containing protein (27 kDa, Protein from Thermochaetoides thermophila DSM 1495)
- Rna exosome core (exo9) (294 kDa, Complex 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 ]
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (8 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Transcription elongation complex with spt4/5 (Complex)
- Dna non-template strand (7 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo12 (5 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Spt4/5 (Complex 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)
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 rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo11 (11 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 rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 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 rpo10 (7 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 rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo1c (44 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 rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt4 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo11 (11 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 rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit beta (127 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 rpo6 (6 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 rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo1c (44 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation factor spt5 (16 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 rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus apo form of rna polymerase contracted clamp conformation (Complex 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 rpo4 (14 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 beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (31 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo10 (7 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo1c (44 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 ]
- Dna-directed rna polymerase subunit rpo1n (103 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Nucleotide strands (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 beta (127 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna template strand (6 kDa, DNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo11 (11 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Pyrococcus furiosus rna polymerase (Complex from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo5 (9 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo7 (21 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Transcription elongation complex (tec) (Complex)
- Dna-directed rna polymerase subunit rpo4 (14 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo6 (6 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Rna (2 kDa, RNA from Pyrococcus furiosus DSM 3638)
- Dna-directed rna polymerase subunit rpo3 (29 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 rpo10 (7 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 rpa34 (55 kDa, Protein 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 rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase i subunit rpa12 (13 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 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 rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 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 rpabc4 (7 kDa, Protein from Homo sapiens)
- Rna polymerase i (Complex 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 ]
- Decamer of human nlrp3 (1 MDa, Complex from Homo sapiens)
- Nlrp3 (Protein from Homo sapiens)