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- [ Pubmed: 36753546 DOI: doi:10.1101/2022.08.29.505764 ]
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- [ Pubmed: 36753546 DOI: doi:10.1101/2022.08.29.505764 ]
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 [ Pubmed: 36753546 DOI: doi:10.1126/sciadv.ade7093 ]
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- 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)
- Rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Dna (37-mer) (57 kDa, DNA from DNA molecule)
- Dna (27-mer) (54 kDa, DNA from synthetic construct)
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 [ Pubmed: 36753546 DOI: doi:10.1126/sciadv.ade7093 ]
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Rna polymerase coreenzyme (Complex from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (125 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 [ Pubmed: 36753546 DOI: doi:10.1126/sciadv.ade7093 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transcription termination factor rho (Complex from Thermus thermophilus HB8)
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 [ Pubmed: 36753546 DOI: doi:10.1126/sciadv.ade7093 ]
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Zinc ion (65 Da, Ligand)
- 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)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
Thermus thermophilus Rho-engaged RNAP elongation complex (composite structure)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8hsr
Q-score: 0.317
Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI
Sci Adv (2023) 9 pp. eade7093-eade7093 [ Pubmed: 36753546 DOI: doi:10.1126/sciadv.ade7093 ]
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transcription termination factor rho (47 kDa, Protein from Thermus thermophilus HB8)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (171 kDa, Protein from Thermus thermophilus HB8)
- Rho-engaged rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Dna (41-mer) (57 kDa, DNA from synthetic construct)
- Dna (31-mer) (54 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Rna (29-mer) (39 kDa, RNA from synthetic construct)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
Detergent-solubilized E. coli RseP in complex with Fab
Imaizumi Y, Takanuki K, Miyake T, Takemoto M, Hirata K, Hirose M, Oi R, Kobayashi T, Miyoshi K, Aruga R, Yokoyama T, Katagiri S, Matsuura H, Iwasaki K, Kato T, Kaneko MK, Kato Y, Tajiri M, Akashi S, Nureki O, Hizukuri Y, Akiyama Y, Nogi T
Sci Adv (2022) 8 pp. eabp9011-eabp9011 [ DOI: doi:10.1126/sciadv.abp9011 Pubmed: 36001659 ]
- Binary complex of e. coli rsep with fab (Complex)
- Light chain of fab (Protein from Mus musculus)
- Heavy chain of fab (Protein from Mus musculus)
- Fab (Complex from Mus musculus)
- Rsep (Complex from Escherichia coli)
- Rsep (Protein from Escherichia coli)
Deterget-solubilized E. coli RseP(L358C) mutant in complex with Fab
Imaizumi Y, Takanuki K, Miyake T, Takemoto M, Hirata K, Hirose M, Oi R, Kobayashi T, Miyoshi K, Aruga R, Yokoyama T, Katagiri S, Matsuura H, Iwasaki K, Kato T, Kaneko MK, Kato Y, Tajiri M, Akashi S, Nureki O, Hizukuri Y, Akiyama Y, Nogi T
Sci Adv (2022) 8 pp. eabp9011-eabp9011 [ DOI: doi:10.1126/sciadv.abp9011 Pubmed: 36001659 ]
- Rsep (Complex from Escherichia coli)
- Binary complex of e. coli rsep(l358c) mutant with fab (Complex)
- E. coli rsep(l358c) mutant (Protein from Escherichia coli)
- Light chain of fab (Protein from Mus musculus)
- Fab (Complex from Mus musculus)
- Heavy chain of fab (Protein from Mus musculus)
Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7dpa
Q-score: 0.239
Kukimoto-Niino M, Katsura K, Kaushik R, Ehara H, Yokoyama T, Uchikubo-Kamo T, Nakagawa R, Mishima-Tsumagari C, Yonemochi M, Ikeda M, Hanada K, Zhang KYJ, Shirouzu M
Sci Adv (2021) 7 [ DOI: doi:10.1126/sciadv.abg3147 Pubmed: 34290093 ]
- Dedicator of cytokinesis protein 5 (191 kDa, Protein from Homo sapiens)
- Engulfment and cell motility protein 1 (84 kDa, Protein from Homo sapiens)
- Ras-related c3 botulinum toxin substrate 1 (20 kDa, Protein from Homo sapiens)
- Elmo1-dock5-rac1 (Complex from Homo sapiens)