Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex
Resolution: 3.78 Å
EM Method: Single-particle
Fitted PDBs: 8yf5
Q-score: 0.391
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- Exonuclease rat1p and rai1p interacting protein (42 kDa, Protein from Komagataella phaffii)
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Komagataella phaffii rat1-rai1-rtt103 complex (Complex from Komagataella phaffii)
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8yfe
Q-score: 0.388
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Komagataella phaffii rat1-rai1 complex (Complex from Komagataella phaffii)
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8yfq
Q-score: 0.393
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- Cryo em structure of komagataella phaffii rnapii-rat1-rai1 pre-termination complex (Complex from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Rna (22-mer) (7 kDa, RNA from synthetic construct)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna (90-mer) (27 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Dna (90-mer) (27 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8yfr
Q-score: 0.366
Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI
Nat Commun (2024) 15 pp. 7854-7854 [ Pubmed: 39245712 DOI: doi:10.1038/s41467-024-52157-0 ]
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii)
- 5'-3' exoribonuclease (115 kDa, Protein from Komagataella phaffii)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii)
- Decapping nuclease (44 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii)
- Komagataella phaffii rat1-rai1 complex bound within the rnapii cleft (Complex from Komagataella phaffii)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii)
- Magnesium ion (24 Da, Ligand)
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii)
Thermus thermophilus Rho-engaged RNAP elongation complex; EC part
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093- [ DOI: doi:10.1101/2022.08.29.505764 Pubmed: 36753546 ]
Thermus thermophilus Rho-engaged RNAP elongation complex; Rho part
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093- [ DOI: doi:10.1101/2022.08.29.505764 Pubmed: 36753546 ]
Thermus thermophilus RNA polymerase elongation complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8hsg
Q-score: 0.434
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Dna (37-mer) (57 kDa, DNA from DNA molecule)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Dna (27-mer) (54 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*cp*cp*ap*cp*ap*up*cp*cp*ap*cp*cp*u)-3') (39 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
Thermus thermophilus RNA polymerase coreenzyme
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8hsh
Q-score: 0.374
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Rna polymerase coreenzyme (Complex from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
Thermus thermophilus transcription termination factor Rho bound with ADP-BeF3
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8hsj
Q-score: 0.235
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Transcription termination factor rho (Complex from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
Thermus thermophilus RNA polymerase bound with an inverted Rho hexamer
Resolution: 5.8 Å
EM Method: Single-particle
Fitted PDBs: 8hsl
Q-score: 0.166
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ DOI: doi:10.1126/sciadv.ade7093 Pubmed: 36753546 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Rna polymerase bound with an inverted rho (Complex from Thermus thermophilus HB8)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)