Structure of the Argonaute protein from Kurthia massiliensis in complex with guide DNA
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8xhv
Q-score: 0.515
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Structure of the argonaute protein from kurthia massiliensis in complex with guide dna (Complex from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8xjx
Q-score: 0.529
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Target dna (5 kDa, DNA from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Kmago (Complex from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 8xk3
Q-score: 0.567
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Target dna-2 (2 kDa, DNA from Kurthia massiliensis)
- Target dna-1 (2 kDa, DNA from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Kmago (Complex from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8xk4
Q-score: 0.513
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
- Kmago (Complex from Kurthia massiliensis)
- Target dna (2 kDa, DNA from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- 2'-deoxycytidine-5'-monophosphate (307 Da, Ligand)
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8xjw
Q-score: 0.503
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Water (18 Da, Ligand)
- Kmago (Complex from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
- Target rna (5 kDa, RNA from Kurthia massiliensis)
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 8xk0
Q-score: 0.55
Tao X, Ding H, Wu S, Wang F, Xu H, Li J, Zhai C, Li S, Chen K, Wu S, Liu Y, Ma L
Nucleic Acids Res (2024) 52 pp. 11895-11910 [ Pubmed: 39315697 DOI: doi:10.1093/nar/gkae820 ]
- Target dna (5 kDa, DNA from Kurthia massiliensis)
- Water (18 Da, Ligand)
- Kmago (Complex from Kurthia massiliensis)
- Kmago (85 kDa, Protein from Kurthia massiliensis)
- Manganese (ii) ion (54 Da, Ligand)
- Guide dna (5 kDa, DNA from Kurthia massiliensis)
Cryo-EM structure of SoxS-dependent transcription activation complex with micF promoter DNA
Resolution: 4.55 Å
EM Method: Single-particle
Fitted PDBs: 7w5w
Q-score: 0.332
Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W
Nucleic Acids Res (2022) 50 pp. 11359-11373 [ DOI: doi:10.1093/nar/gkac898 Pubmed: 36243985 ]
- Dna (Complex)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Soxs-dependent transcription activation complex with micf promoter dna (Complex from Escherichia coli K-12)
- Micf promoter dna forward strand (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna reverse strand (21 kDa, DNA from Escherichia coli)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of SoxS-dependent transcription activation complex with zwf promoter DNA
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7w5x
Q-score: 0.47
Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W
Nucleic Acids Res (2022) 50 pp. 11359-11373 [ DOI: doi:10.1093/nar/gkac898 Pubmed: 36243985 ]
- Soxs-dependent transcription activation complex with zwf promoter dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Zwf promoter dna reverse strand (23 kDa, DNA from Escherichia coli)
- Dna (Complex)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Zwf promoter dna forward strand (23 kDa, DNA from Escherichia coli)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of SoxS-dependent transcription activation complex with fpr promoter DNA
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7w5y
Q-score: 0.369
Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W
Nucleic Acids Res (2022) 50 pp. 11359-11373 [ Pubmed: 36243985 DOI: doi:10.1093/nar/gkac898 ]
- Dna (Complex)
- Fpr promoter dna forward strand (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Fpr promoter dna reverse strand (26 kDa, DNA from Escherichia coli)
- Soxs-dependent transcription activation complex with fpr promoter dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation
Resolution: 4.57 Å
EM Method: Single-particle
Fitted PDBs: 7vwy
Q-score: 0.359
Shi J, Wang F, Li F, Wang L, Xiong Y, Wen A, Jin Y, Jin S, Gao F, Feng Z, Li J, Zhang Y, Shang Z, Wang S, Feng Y, Lin W
Nucleic Acids Res (2022) 50 pp. 5974-5987 [ DOI: doi:10.1093/nar/gkac433 Pubmed: 35641097 ]
- Zinc ion (65 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna scaffold reverse strand (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Rob-dependent transcription activation complex (Complex from Escherichia coli)
- Right origin-binding protein (33 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna scaffold forward strand (21 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)