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)
Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8efv
Q-score: 0.556
Rish AD, Shen Z, Chen Z, Zhang N, Zheng Q, Fu TM
Nat Commun (2023) 14 pp. 3549-3549 [ Pubmed: 37322069 DOI: doi:10.1038/s41467-023-39250-6 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Single homo-hexameric aaa+ atpase ruvb motor (Complex from Thermus thermophilus HB8)
- 49-mer dna (15 kDa, DNA from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Holliday junction atp-dependent dna helicase ruvb (36 kDa, Protein from Thermus thermophilus HB8)
- 51-mer dna (15 kDa, DNA from Thermus thermophilus HB8)
Structure of double homo-hexameric AAA+ ATPase RuvB motors
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8efy
Q-score: 0.531
Rish AD, Shen Z, Chen Z, Zhang N, Zheng Q, Fu TM
Nat Commun (2023) 14 pp. 3549-3549 [ Pubmed: 37322069 DOI: doi:10.1038/s41467-023-39250-6 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- Ssdna (15 kDa, DNA from Thermus thermophilus HB8)
- Ssdna (15 kDa, DNA from Thermus thermophilus HB8)
- Magnesium ion (24 Da, Ligand)
- Double homo-hexameric aaa+ atpase ruvb motors (Complex from Thermus thermophilus HB8)
- Holliday junction atp-dependent dna helicase ruvb (36 kDa, Protein from Thermus thermophilus HB8)
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)
Complex of RecF and DNA from Thermus thermophilus.
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8a8j
Q-score: 0.556
Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M
Nat Struct Mol Biol (2023) 30 pp. 650-660 [ DOI: doi:10.1038/s41594-023-00967-z Pubmed: 37081315 ]
- Complex of recf and dna from thermus thermophilus. (95 kDa, Complex from Thermus thermophilus HB8)
- Oligo2 (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna replication and repair protein recf (37 kDa, Protein from Thermus thermophilus HB8)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Oligo1 (7 kDa, DNA from synthetic construct)
Complex of RecF-RecR-DNA from Thermus thermophilus.
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8a93
Q-score: 0.525
Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M
Nat Struct Mol Biol (2023) 30 pp. 650-660 [ DOI: doi:10.1038/s41594-023-00967-z Pubmed: 37081315 ]
- Dna replication and repair protein recf (37 kDa, Protein from Thermus thermophilus HB8)
- Recombination protein recr (21 kDa, Protein from Thermus thermophilus HB8)
- Oligo2 (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Complex of recf-recr-dna from thermus thermophilus. (180 kDa, Complex from Thermus thermophilus HB8)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Oligo1 (7 kDa, DNA from synthetic construct)