The isolated Vo domain of V/A-ATPase from Thermus thermophilus.
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ywt
Q-score: 0.476
Kishikawa JI, Nishida Y, Nakano A, Kato T, Mitsuoka K, Okazaki KI, Yokoyama K
Nat Commun (2024) 15 pp. 9883-9883 [ Pubmed: 39567487 DOI: doi:10.1038/s41467-024-53504-x ]
- V-type atp synthase, subunit k (10 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit c (35 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit i (72 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase, subunit (vapc-therm) (13 kDa, Protein from Thermus thermophilus HB8)
- The isolated vo domain of v/a-atpase from thermus thermophilus (300 kDa, Complex from Thermus thermophilus HB8)
- Water (18 Da, Ligand)
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)
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 [ 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)
- Dna (41-mer) (57 kDa, DNA from synthetic construct)
- Dna (31-mer) (54 kDa, DNA from synthetic construct)
- Rna (29-mer) (39 kDa, RNA from synthetic construct)
- 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)
- Rho-engaged rna polymerase elongation complex (Complex from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7val
Q-score: 0.545
Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K
Nat Commun (2022) 13 pp. 1213-1213 [ Pubmed: 35260556 DOI: doi:10.1038/s41467-022-28832-5 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- V-type atp synthase subunit g (13 kDa, Protein from Thermus thermophilus HB8)
- V1eg of v/a-atpase from thermus thermophilus, high atp, state1-1 (400 kDa, Complex from Thermus thermophilus HB8)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state1-2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7vam
Q-score: 0.54
Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K
Nat Commun (2022) 13 pp. 1213-1213 [ Pubmed: 35260556 DOI: doi:10.1038/s41467-022-28832-5 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- V-type atp synthase, subunit g (13 kDa, Protein from Thermus thermophilus HB8)
- V1eg of v/a-atpase from thermus thermophilus, high atp, state1-2 (400 kDa, Complex from Thermus thermophilus HB8)
V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state2-1
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7van
Q-score: 0.518
Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K
Nat Commun (2022) 13 pp. 1213-1213 [ Pubmed: 35260556 DOI: doi:10.1038/s41467-022-28832-5 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V1eg of v/a-atpase from thermus thermophilus, high atp, state2-1 (400 kDa, Complex from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- V-type atp synthase, subunit g (13 kDa, Protein from Thermus thermophilus HB8)
V1EG of V/A-ATPase from Thermus thermophilus, high ATP, state2-2
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7vao
Q-score: 0.474
Kishikawa J, Nakanishi A, Nakano A, Saeki S, Furuta A, Kato T, Mistuoka K, Yokoyama K
Nat Commun (2022) 13 pp. 1213-1213 [ Pubmed: 35260556 DOI: doi:10.1038/s41467-022-28832-5 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- V-type atp synthase beta chain (53 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase alpha chain (63 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit e (20 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit f (11 kDa, Protein from Thermus thermophilus HB8)
- V-type atp synthase subunit d (24 kDa, Protein from Thermus thermophilus HB8)
- V1eg of v/a-atpase from thermus thermophilus, high atp, state2-2 (400 kDa, Complex from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- V-type atp synthase, subunit g (13 kDa, Protein from Thermus thermophilus HB8)