Allostery through DNA drives phenotype switching
Resolution: 5.7 Å
EM Method: Single-particle
Fitted PDBs: 6z0s
Q-score: 0.221
Rosenblum G, Elad N, Rozenberg H, Wiggers F, Jungwirth J, Hofmann H
Nat Commun (2021) 12 pp. 2967-2967 [ DOI: doi:10.1038/s41467-021-23148-2 Pubmed: 34016970 ]
- Comk transcription factor bound to its comg promoter dna. (Complex from Bacillus subtilis)
- Comg promoter dna - strand b (28 kDa, DNA from Bacillus subtilis)
- Comg promoter dna - strand a (28 kDa, DNA from Bacillus subtilis)
Allostery through DNA drives phenotype switching
Resolution: 7.0 Å
EM Method: Single-particle
Fitted PDBs: 7nbn
Q-score: 0.196
Rosenblum G, Elad N, Rozenberg H, Wiggers F, Jungwirth J, Hofmann H
Nat Commun (2021) 12 pp. 2967-2967 [ DOI: doi:10.1038/s41467-021-23148-2 Pubmed: 34016970 ]
- Comk transcription factor bound to its comg promoter dna. (Complex from Bacillus subtilis)
- Addab promoter (24 kDa, DNA from Bacillus subtilis)
- Addab promoter (23 kDa, DNA from Bacillus subtilis)
Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 6zj3
Q-score: 0.548
Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M
Nucleic Acids Res (2020) 48 pp. 11750-11761 [ DOI: doi:10.1093/nar/gkaa893 Pubmed: 33091122 ]
- Ribosomal protein el37 (13 kDa, Protein from Euglena gracilis)
- A-site trna (3 kDa, RNA from Euglena gracilis)
- 60s ribosomal protein l7a (32 kDa, Protein from Euglena gracilis)
- Ribosomal protein el39 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein es7 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul23 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein us15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul30 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul14 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein el18 (21 kDa, Protein from Euglena gracilis)
- 5s rrna (38 kDa, RNA from Euglena gracilis)
- Ribosomal protein el19 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul6 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul18 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul29 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul24 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es24 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es1 (28 kDa, Protein from Euglena gracilis)
- 5.8s rrna (52 kDa, RNA from Euglena gracilis)
- P-trna (24 kDa, RNA from Euglena gracilis)
- Water (18 Da, Ligand)
- Lsu rrna chain 5 (170 kDa, RNA from Euglena gracilis)
- Ribosomal protein el29 (13 kDa, Protein from Euglena gracilis)
- A-trna (24 kDa, RNA from Euglena gracilis)
- Ribosomal protein el6 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr2 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein el30 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein eseug1 (32 kDa, Protein from Euglena gracilis)
- Ribosomal protein el13 (25 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 6 (75 kDa, RNA from Euglena gracilis)
- Ribosomal protein es31 (17 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 4 (225 kDa, RNA from Euglena gracilis)
- Ribosomal protein es10 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el40 (14 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 8 (199 kDa, RNA from Euglena gracilis)
- Ribosomal protein es4 (31 kDa, Protein from Euglena gracilis)
- Euglena gracilis 80s ribosome (Complex from Euglena gracilis)
- Ribosomal protein elegr1 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein es21 (10 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 7 (240 kDa, RNA from Euglena gracilis)
- Ribosomal protein ul13 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul3 (46 kDa, Protein from Euglena gracilis)
- Ribosomal protein el31 (17 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 10 (20 kDa, RNA from Euglena gracilis)
- Ribosomal protein el15 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein el21 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein us2 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein es26 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein es27 (9 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 2 (113 kDa, RNA from Euglena gracilis)
- Ribosomal protein ul5 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein us13 (17 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 12 (18 kDa, RNA from Euglena gracilis)
- 60s ribosomal protein l10 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein es8 (35 kDa, Protein from Euglena gracilis)
- Ribosomal protein el24 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el38 (9 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 13 (27 kDa, RNA from Euglena gracilis)
- Ribosomal protein el41 (4 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr3 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein es25 (13 kDa, Protein from Euglena gracilis)
- Rack1 (34 kDa, Protein from Euglena gracilis)
- Ribosomal protein el20 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein us8 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein us19 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein es28 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein us14 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein us5 (27 kDa, Protein from Euglena gracilis)
- Ribosomal protein es12 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein us3 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein el42 (10 kDa, Protein from Euglena gracilis)
- Ribosomal protein el43 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein el34 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein us9 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el33 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein us7 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein el22 (18 kDa, Protein from Euglena gracilis)
- 18s rrna (747 kDa, RNA from Euglena gracilis)
- Ribosomal protein el36 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein es6 (31 kDa, Protein from Euglena gracilis)
- Ribosomal protein el32 (16 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 1 (42 kDa, RNA from Euglena gracilis)
- Ribosomal protein ul4 (41 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul2 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein es17 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul22 (18 kDa, Protein from Euglena gracilis)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein el14 (25 kDa, Protein from Euglena gracilis)
- Ribosomal protein us10 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein us11 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es19 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein us4 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein es30 (7 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 3 (37 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 11 (30 kDa, RNA from Euglena gracilis)
- E-trna (24 kDa, RNA from Euglena gracilis)
- Ribosomal protein el27 (15 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 9 (52 kDa, RNA from Euglena gracilis)
- Ribosomal protein us17 (19 kDa, Protein from Euglena gracilis)
- Ribosomal protein us12 (15 kDa, Protein from Euglena gracilis)
Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6az1
Q-score: 0.566
Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G
Nat Commun (2017) 8 pp. 1589-1589 [ Pubmed: 29150609 DOI: doi:10.1038/s41467-017-01664-4 ]
- Ribosomal protein s14 (6 kDa, Protein from Leishmania donovani)
- Ribosomal protein s15 (17 kDa, Protein from Leishmania donovani)
- Ribosomal protein s9 (16 kDa, Protein from Leishmania donovani)
- Ribosomal protein s19e (20 kDa, Protein from Leishmania donovani)
- Ribosomal protein s21e (16 kDa, Protein from Leishmania donovani)
- Ribosomal protein s27e (9 kDa, Protein from Leishmania donovani)
- P-site trna (24 kDa, RNA from Escherichia coli)
- Ribosomal protein s13 (17 kDa, Protein from Leishmania donovani)
- Ribosomal protein s4e (30 kDa, Protein from Leishmania donovani)
- Ribosomal protein s12e (15 kDa, Protein from Leishmania donovani)
- Ribosomal protein s3 (24 kDa, Protein from Leishmania donovani)
- Ribosomal protein s26e (12 kDa, Protein from Leishmania donovani)
- Ribosomal protein s30e (7 kDa, Protein from Leishmania donovani)
- Ribosomal protein s7e (23 kDa, Protein from Leishmania donovani)
- Magnesium ion (24 Da, Ligand)
- Paromomycin (615 Da, Ligand)
- Ribosomal protein s8 (14 kDa, Protein from Leishmania donovani)
- Ribosomal protein s31e (17 kDa, Protein from Leishmania donovani)
- Ribosomal protein s1e (30 kDa, Protein from Leishmania donovani)
- E-site trna (24 kDa, RNA from Escherichia coli)
- Lack1 (34 kDa, Protein from Leishmania donovani)
- Ribosomal protein s17e (16 kDa, Protein from Leishmania donovani)
- Ribosomal protein s12 (15 kDa, Protein from Leishmania donovani)
- Ribosomal protein s7 (21 kDa, Protein from Leishmania donovani)
- Ribosomal protein s17 (19 kDa, Protein from Leishmania donovani)
- Leishmania donovani 91s ribosome ssu (Complex from Leishmania donovani)
- Ribosomal protein s6e (28 kDa, Protein from Leishmania donovani)
- Ribosomal protein s24e (15 kDa, Protein from Leishmania donovani)
- Ribosomal protein s10 (13 kDa, Protein from Leishmania donovani)
- Ribosomal protein s25e (13 kDa, Protein from Leishmania donovani)
- Ribosomal rna 18s (710 kDa, RNA from Leishmania donovani)
- Ribosomal protein s2 (27 kDa, Protein from Leishmania donovani)
- Ribosomal protein s4 (22 kDa, Protein from Leishmania donovani)
- Ribosomal protein s10e (17 kDa, Protein from Leishmania donovani)
- Mrna (4 kDa, RNA from Leishmania donovani)
- Ribosomal protein s5 (28 kDa, Protein from Leishmania donovani)
- Water (18 Da, Ligand)
- Ribosomal protein s8e (25 kDa, Protein from Leishmania donovani)
- Ribosomal protein s11 (15 kDa, Protein from Leishmania donovani)
- Ribosomal protein s28e (9 kDa, Protein from Leishmania donovani)
- Trna-phe (24 kDa, RNA from Escherichia coli)
- Ribosomal protein s19 (17 kDa, Protein from Leishmania donovani)
Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6az3
Q-score: 0.599
Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G
Nat Commun (2017) 8 pp. 1589-1589 [ Pubmed: 29150609 DOI: doi:10.1038/s41467-017-01664-4 ]
- Ribosomal protein l1a, putative (40 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l29 (7 kDa, Protein from Leishmania donovani)
- Leishmania donovani 91s ribosome lsu (Complex from Leishmania donovani)
- Ribosomal protein ul3 (45 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l37 (9 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l9, putative (21 kDa, Protein from Leishmania donovani)
- Rrna 5.8s (54 kDa, RNA from Leishmania donovani)
- Ribosomal protein el6 (21 kDa, Protein from Leishmania donovani)
- Ribosomal protein el24 (7 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l39, putative (6 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l37a (10 kDa, Protein from Leishmania donovani)
- Rrna zeta (22 kDa, RNA from Leishmania donovani)
- Ribosomal protein el41 (4 kDa, Protein from Leishmania donovani)
- Rrna delta (59 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l11 (l5, l16) (19 kDa, Protein from Leishmania donovani)
- Rrna 5s (37 kDa, RNA from Leishmania donovani)
- Ribosomal protein l35ae family protein (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l18, putative (21 kDa, Protein from Leishmania donovani)
- Ribosomal l38e family protein (8 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l7 family protein (26 kDa, Protein from Leishmania donovani)
- Paromomycin (615 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l21, putative (17 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l23a, putative (13 kDa, Protein from Leishmania donovani)
- Rrna epsilon (42 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l5, putative (34 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l17, putative (17 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l30 (10 kDa, Protein from Leishmania donovani)
- Ribosomal protein ul2 (27 kDa, Protein from Leishmania donovani)
- 60s_ribosomal_protein_l32/genedb:lmjf.21.1720 (15 kDa, Protein from Leishmania donovani)
- Ribosomal l27e family protein (15 kDa, Protein from Leishmania donovani)
- Rrna gamma (67 kDa, RNA from Leishmania donovani)
- 60s ribosomal subunit protein l31, putative (13 kDa, Protein from Leishmania donovani)
- Ribosomal protein el13 (23 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l10, putative (24 kDa, Protein from Leishmania donovani)
- Ribosomal protein ul24 (13 kDa, Protein from Leishmania donovani)
- Ribosomal protein l15 (24 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l18a (20 kDa, Protein from Leishmania donovani)
- 60s_ribosomal_protein_l35_putative/genedb:lmjf.26.2330/genedb:lmjf.26.2340 (14 kDa, Protein from Leishmania donovani)
- Ribosomal protein ul13 (25 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l7a (39 kDa, Protein from Leishmania donovani)
- Ubiquitin-60s ribosomal protein l40 (5 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l28, putative (15 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l36, putative (11 kDa, Protein from Leishmania donovani)
- Rrna alpha (575 kDa, RNA from Leishmania donovani)
- Ribosomal protein l19e family protein (22 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l34, putative (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l22, putative (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l44, putative (11 kDa, Protein from Leishmania donovani)
- Rrna beta (492 kDa, RNA from Leishmania donovani)
- Water (18 Da, Ligand)
- 60s ribosomal protein l23, putative (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l27a/l29, putative (16 kDa, Protein from Leishmania donovani)
- Probable 60s ribosomal protein l14 (17 kDa, Protein from Leishmania donovani)
Cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 3jcs
Q-score: 0.499
Shalev-Benami M, Zhang Y, Matzov D, Halfon Y, Zackay A, Rozenberg H, Zimmerman E, Bashan A, Jaffe CL, Yonath A, Skiniotis G
Cell Rep (2016) 16 pp. 288-294 [ Pubmed: 27373148 DOI: doi:10.1016/j.celrep.2016.06.014 ]