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 [ Pubmed: 36243985 DOI: doi:10.1093/nar/gkac898 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna (Complex)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna reverse strand (21 kDa, DNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- Soxs-dependent transcription activation complex with micf promoter dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
- Micf promoter dna forward strand (21 kDa, DNA from Escherichia coli)
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 [ Pubmed: 36243985 DOI: doi:10.1093/nar/gkac898 ]
- Dna-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna (Complex)
- 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)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Zwf promoter dna reverse strand (23 kDa, DNA from Escherichia coli)
- Soxs-dependent transcription activation complex with zwf promoter dna (Complex from Escherichia coli K-12)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Zwf promoter dna forward strand (23 kDa, DNA from Escherichia coli)
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-directed rna polymerase subunit omega (10 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit alpha (36 kDa, Protein from Escherichia coli K-12)
- Dna (Complex)
- Rna polymerase sigma factor rpod (70 kDa, Protein from Escherichia coli K-12)
- Soxs-dependent transcription activation complex with fpr promoter dna (Complex from Escherichia coli K-12)
- Regulatory protein soxs (12 kDa, Protein from Escherichia coli K-12)
- Dna-directed rna polymerase subunit beta' (155 kDa, Protein from Escherichia coli K-12)
- Fpr promoter dna reverse strand (26 kDa, DNA from Escherichia coli)
- Dna-directed rna polymerase subunits (Complex from Escherichia coli)
- Dna-directed rna polymerase subunit beta (150 kDa, Protein from Escherichia coli K-12)
- Fpr promoter dna forward strand (26 kDa, DNA from Escherichia coli)
Human Tom70 in complex with SARS CoV2 Orf9b
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7kdt
Q-score: 0.473
Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Huttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbolle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss 3rd FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech Jr TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, Garcia-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ
Science (2020) 370 [ DOI: doi:10.1126/science.abe9403 Pubmed: 33060197 ]
- Orf9b protein (10 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Mitochondrial import receptor subunit tom70 (56 kDa, Protein from Homo sapiens)
- Orf9b-tom70 complex (Complex from Homo sapiens)
human KCC1 structure determined in KCl and detergent GDN
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6kkr
Q-score: 0.559
Liu S, Chang S, Han B, Xu L, Zhang M, Zhao C, Yang W, Wang F, Li J, Delpire E, Ye S, Bai XC, Guo J
Science (2019) 366 pp. 505-508 [ Pubmed: 31649201 DOI: doi:10.1126/science.aay3129 ]
- Potassium ion (39 Da, Ligand)
- Solute carrier family 12 member 4 (122 kDa, Protein from Homo sapiens)
- Potassium chloride co-transporter 1 (Complex from Homo sapiens)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Chloride ion (35 Da, Ligand)
human KCC1 structure determined in KCl and lipid nanodisc
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 6kkt
Q-score: 0.559
Liu S, Chang S, Han B, Xu L, Zhang M, Zhao C, Yang W, Wang F, Li J, Delpire E, Ye S, Bai XC, Guo J
Science (2019) 366 pp. 505-508 [ Pubmed: 31649201 DOI: doi:10.1126/science.aay3129 ]
- Potassium ion (39 Da, Ligand)
- Solute carrier family 12 member 4 (122 kDa, Protein from Homo sapiens)
- Potassium chloride co-transporter 1 (Complex from Homo sapiens)
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Chloride ion (35 Da, Ligand)
human KCC1 structure determined in NaCl and GDN
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6kku
Q-score: 0.469
Liu S, Chang S, Han B, Xu L, Zhang M, Zhao C, Yang W, Wang F, Li J, Delpire E, Ye S, Bai XC, Guo J
Science (2019) 366 pp. 505-508 [ Pubmed: 31649201 DOI: doi:10.1126/science.aay3129 ]
- 2-[2-[(1~{s},2~{s},4~{s},5'~{r},6~{r},7~{s},8~{r},9~{s},12~{s},13~{r},16~{s})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol (516 Da, Ligand)
- Potassium chloride co-transporter 1 (Complex from Homo sapiens)
- Solute carrier family 12 member 4 (122 kDa, Protein from Homo sapiens)
- Chloride ion (35 Da, Ligand)