Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8dy7
Q-score: 0.482
Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA
PNAS (2023) 120 pp. e2220785120-e2220785120 [ DOI: doi:10.1073/pnas.2220785120 Pubmed: 36888660 ]
- Iron/sulfur cluster (351 Da, Ligand)
- Transcriptional regulator whib (10 kDa, Protein from Streptomyces venezuelae)
- Dna (78-mer) (30 kDa, DNA from Streptomyces venezuelae)
- Dna (71-mer) (30 kDa, DNA from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit beta' (144 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Streptomyces venezuelae)
- Probable cell division protein whia (37 kDa, Protein from Streptomyces venezuelae)
- Rna polymerase sigma factor siga (56 kDa, Protein from Streptomyces venezuelae)
- Rna polymerase-binding protein rbpa (14 kDa, Protein from Streptomyces venezuelae)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Streptomyces venezuelae)
- Dna-directed rna polymerase subunit omega (9 kDa, Protein from Streptomyces venezuelae)
- Streptomyces venezuelae rnap transcription open promoter complex with whia and whib transcription factors (Complex from Streptomyces venezuelae)
ATP and DNA bound SMC5/6 core complex
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7tve
Q-score: 0.378
Yu Y, Li S, Ser Z, Kuang H, Than T, Guan D, Zhao X, Patel DJ
PNAS (2022) 119 pp. e2202799119-e2202799119 [ DOI: doi:10.1073/pnas.2202799119 Pubmed: 35648833 ]
- Dna (68-mer) (21 kDa, DNA from synthetic construct)
- Non-structural maintenance of chromosomes element 1 (38 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Hexamer complex of smc5-smc6-nse1-nse3-nse4-nse2 with atp and dna (410 kDa, Complex from Saccharomyces cerevisiae W303)
- Dna (78-mer) (23 kDa, DNA from synthetic construct)
- Structural maintenance of chromosomes protein 6 (132 kDa, Protein from Saccharomyces cerevisiae W303)
- Non-structural maintenance of chromosome element 4 (46 kDa, Protein from Saccharomyces cerevisiae W303)
- Non-structural maintenance of chromosome element 3 (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Structural maintenance of chromosomes protein 5 (126 kDa, Protein from Saccharomyces cerevisiae W303)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 6pb4
Q-score: 0.224
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol (2020) 18 pp. e3000706- [ DOI: doi:10.1371/journal.pbio.3000706 ]
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna/rna (Complex)
- Dna-directed rna polymerase subunit alpha, dna-directed rna polymerase subunit beta, dna-directed rna polymerase subunit beta', dna-directed rna polymerase subunit omega, rna polymerase sigma factor rpod, camp-activated global transcriptional regulator crp (Complex from Escherichia coli)
- Synthetic template strand dna (78-mer) (24 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-3',5'-cyclic-monophosphate (329 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Synthetic nontemplate strand dna (78-mer) (23 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Camp-activated global transcriptional regulator crp (23 kDa, Protein from Escherichia coli)
- Nascent rna (1 kDa, RNA from Escherichia coli)
- The e. coli class-ii cap-dependent transcription activation complex with de novo rna transcript at the state 2 (550 kDa, Complex from Escherichia coli)
The E. coli class-II CAP-dependent transcription activation complex at the state 1 architecture
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 6pb5
Q-score: 0.082
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol (2020) 18 pp. e3000706- [ DOI: doi:10.1371/journal.pbio.3000706 ]
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- The e coli class-ii cap-dependent transcription activation complex at the state 1 (550 kDa, Complex from Escherichia coli)
- Synthetic template strand dna (78-mer) (24 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Adenosine-3',5'-cyclic-monophosphate (329 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Synthetic nontemplate strand dna (78-mer) (23 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Camp-activated global transcriptional regulator crp (23 kDa, Protein from Escherichia coli)
The E. coli class-II CAP-dependent transcription activation complex at the state 2
Resolution: 4.29 Å
EM Method: Single-particle
Fitted PDBs: 6pb6
Q-score: 0.223
Shi W, Jiang Y, Deng Y, Dong Z, Liu B
PLoS Biol (2020) 18 pp. e3000706- [ DOI: doi:10.1371/journal.pbio.3000706 ]
- The e. coli class-ii cap-dependent transcription activation complex at the state 2 (550 kDa, Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli)
- Rna polymerase sigma factor rpod (72 kDa, Protein from Escherichia coli)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli)
- Synthetic nontemplate strand dna (78-mer) (23 kDa, DNA from Escherichia coli)
- Camp-activated global transcriptional regulator crp (23 kDa, Protein from Escherichia coli)
- Synthetic template strand dna (78-mer) (24 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunit alpha, dna-directed rna polymerase subunit beta, dna-directed rna polymerase subunit beta', dna-directed rna polymerase subunit omega, rna polymerase sigma factor rpod, camp-activated global transcriptional regulator crp (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Adenosine-3',5'-cyclic-monophosphate (329 Da, Ligand)
- Dna (Complex)