Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6zy5
Q-score: 0.385
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V
Nat Commun (2021) 12 pp. 2962-2962 [ DOI: doi:10.1038/s41467-021-23136-6 Pubmed: 34016969 ]
- Etoposide-bound human top2a dna-binding/cleavage domain in state 1 (205 kDa, Complex)
- Dna topoisomerase 2-alpha (174 kDa, Protein from Homo sapiens)
- Dna (5'-d(*gp*ap*gp*gp*ap*tp*gp*ap*cp*gp*ap*tp*g)-3') (4 kDa, DNA from Homo sapiens)
- Dna topoisomerase 2-alpha (Complex from Homo sapiens)
- Dna (5'-d(*cp*gp*cp*gp*cp*ap*tp*cp*gp*tp*cp*ap*tp*cp*cp*tp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-o-[(1r)-ethylidene]-beta-d-glucopyranoside (588 Da, Ligand)
Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 2
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6zy6
Q-score: 0.272
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V
Nat Commun (2021) 12 pp. 2962-2962 [ DOI: doi:10.1038/s41467-021-23136-6 Pubmed: 34016969 ]
- Dna topoisomerase 2-alpha (174 kDa, Protein from Homo sapiens)
- Dna (5'-d(*gp*ap*gp*gp*ap*tp*gp*ap*cp*gp*ap*tp*g)-3') (4 kDa, DNA from Homo sapiens)
- Etoposide-bound human top2a dna-binding/cleavage domain in state 2 (205 kDa, Complex)
- Dna topoisomerase 2-alpha (Complex from Homo sapiens)
- Dna (5'-d(*cp*gp*cp*gp*cp*ap*tp*cp*gp*tp*cp*ap*tp*cp*cp*tp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-o-[(1r)-ethylidene]-beta-d-glucopyranoside (588 Da, Ligand)
Entire Human Top2a - Interface between ATPase and DNA-binding/cleavage domains
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V
Nat Commun (2021) 12 pp. 2962-2962 [ DOI: doi:10.1038/s41467-021-23136-6 Pubmed: 34016969 ]
- Human top2a (Protein from Homo sapiens)
- Etoposide-bound entire human top2a (280 kDa, Complex from Homo sapiens)
Cryo-EM structure of the entire Human topoisomerase II alpha in State 1
Resolution: 4.64 Å
EM Method: Single-particle
Fitted PDBs: 6zy7
Q-score: 0.163
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V
Nat Commun (2021) 12 pp. 2962-2962 [ DOI: doi:10.1038/s41467-021-23136-6 Pubmed: 34016969 ]
- Dna topoisomerase 2-alpha (174 kDa, Protein from Homo sapiens)
- Etoposide-bound entire human top2a in state 1 (205 kDa, Complex)
- Dna (5'-d(*gp*ap*gp*gp*ap*tp*gp*ap*cp*gp*ap*tp*g)-3') (4 kDa, DNA from Homo sapiens)
- Dna topoisomerase 2-alpha (Complex from Homo sapiens)
- Dna (5'-d(*cp*gp*cp*gp*cp*ap*tp*cp*gp*tp*cp*ap*tp*cp*cp*tp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-o-[(1r)-ethylidene]-beta-d-glucopyranoside (588 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
Cryo-EM structure of the entire Human topoisomerase II alpha in State 2
Resolution: 7.4 Å
EM Method: Single-particle
Fitted PDBs: 6zy8
Q-score: 0.122
Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V
Nat Commun (2021) 12 pp. 2962-2962 [ DOI: doi:10.1038/s41467-021-23136-6 Pubmed: 34016969 ]
- Dna topoisomerase 2-alpha (174 kDa, Protein from Homo sapiens)
- Dna (5'-d(*gp*ap*gp*gp*ap*tp*gp*ap*cp*gp*ap*tp*g)-3') (4 kDa, DNA from Homo sapiens)
- Dna topoisomerase 2-alpha (Complex from Homo sapiens)
- Etoposide-bound entire human top2a in state 2 (295 kDa, Complex)
- Dna (5'-d(*cp*gp*cp*gp*cp*ap*tp*cp*gp*tp*cp*ap*tp*cp*cp*tp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (Complex from Homo sapiens)
- (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-o-[(1r)-ethylidene]-beta-d-glucopyranoside (588 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6rks
Q-score: 0.441
Vanden Broeck A, Lotz C, Ortiz J, Lamour V
Nat Commun (2019) 10 pp. 4935-4935 [ DOI: doi:10.1038/s41467-019-12914-y Pubmed: 31666516 ]
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli K-12)
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli K-12)
- Dna binding and cleavage domain of the e. coli dna gyrase in state 1 (Complex)
- Dna strand 2 (5 kDa, DNA from Escherichia coli)
- (3~{r})-3-[[4-(3,4-dihydro-2~{h}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione (448 Da, Ligand)
- Dna binding and cleavage domain of the e. coli dna gyrase in state 1 (Complex from Escherichia coli)
- Dna binding and cleavage domain of the e. coli dna gyrase in state 1 (Complex from Escherichia coli O157:H7 str. SS52)
- Dna strand 1 (4 kDa, DNA from Escherichia coli)
- Dna binding and cleavage domain of the e. coli dna gyrase in state 1 (Complex from Escherichia coli K-12)
E. coli DNA Gyrase - DNA binding and cleavage domain in State 1
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6rku
Q-score: 0.386
Vanden Broeck A, Lotz C, Ortiz J, Lamour V
Nat Commun (2019) 10 pp. 4935-4935 [ DOI: doi:10.1038/s41467-019-12914-y Pubmed: 31666516 ]
- Dna binding and cleavage domain of the e. coli dna gyrase in state 1 (Complex)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli (strain K12))
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli (strain K12))
- Dna strand 2 (5 kDa, DNA from Escherichia coli)
- Dna (Complex from Escherichia coli)
- (3~{r})-3-[[4-(3,4-dihydro-2~{h}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione (448 Da, Ligand)
- Dna strand 1 (4 kDa, DNA from Escherichia coli)
- Dna gyrase (Complex from Escherichia coli K-12)
E. coli DNA Gyrase - DNA binding and cleavage domain in State 2
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6rkv
Q-score: 0.265
Vanden Broeck A, Lotz C, Ortiz J, Lamour V
Nat Commun (2019) 10 pp. 4935-4935 [ DOI: doi:10.1038/s41467-019-12914-y Pubmed: 31666516 ]
- Dna strand 1 (4 kDa, DNA from Escherichia coli (strain K12))
- Dna binding and cleavage domain of the e. coli dna gyrase in state 2 (Complex)
- Dna (Complex from Escherichia coli K-12)
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli (strain K12))
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli (strain K12))
- Dna strand 2 (5 kDa, DNA from Escherichia coli (strain K12))
- Dna gyrase (Complex from Escherichia coli K-12)
CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex
Resolution: 6.6 Å
EM Method: Single-particle
Fitted PDBs: 6rkw
Q-score: 0.128
Vanden Broeck A, Lotz C, Ortiz J, Lamour V
Nat Commun (2019) 10 pp. 4935-4935 [ DOI: doi:10.1038/s41467-019-12914-y Pubmed: 31666516 ]
- Dna gyrase subunit b (Complex from Escherichia coli K-12)
- The complete e. coli dna gyrase complex bound to 130bp dna duplex (470 kDa, Complex)
- Dna (62-mer) (19 kDa, DNA from Escherichia coli)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli (strain K12))
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli (strain K12))
- Dna gyrase subunit a (Complex from Escherichia coli K-12)
- Dna (Complex from Escherichia coli)
- (3~{r})-3-[[4-(3,4-dihydro-2~{h}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione (448 Da, Ligand)
- Dna (58-mer) (17 kDa, DNA from Escherichia coli)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
E. coli DNA Gyrase - ATPase DNA binding and cleavage domains
Vanden Broeck A, Lotz C, Ortiz J, Lamour V
Nat Commun (2019) 10 pp. 4935-4935 [ DOI: doi:10.1038/s41467-019-12914-y Pubmed: 31666516 ]