Cryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4p
Resolution: 2.75 Å
EM Method: Single-particle
Fitted PDBs: 9eyi
Q-score: 0.53
Smalakyte D, Ruksenaite A, Sasnauskas G, Tamulaitiene G, Tamulaitis G
Mol Cell (2024) 84 pp. 4239-4255.e8 [ Pubmed: 39362215 DOI: doi:10.1016/j.molcel.2024.09.002 ]
- Filament fragment of a4p bound ccacalpl (Complex)
- A4p (Complex from synthetic construct)
- Ccacalpl (Complex from Candidatus Cloacimonas acidaminovorans)
- A4p (5'-r(*ap*ap*ap*ap)-3') (1 kDa, RNA from synthetic construct)
- Smods-associated and fused to various effectors domain-containing protein (63 kDa, Protein from Candidatus Cloacimonas acidaminovorans)
Cryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to cA4
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 9eyj
Q-score: 0.475
Smalakyte D, Ruksenaite A, Sasnauskas G, Tamulaitiene G, Tamulaitis G
Mol Cell (2024) 84 pp. 4239-4255.e8 [ Pubmed: 39362215 DOI: doi:10.1016/j.molcel.2024.09.002 ]
- Ca4 (1 kDa, RNA from synthetic construct)
- Filament fragment of ca4 bound ccacalpl (Complex)
- Ccacalpl (Complex from Candidatus Cloacimonas acidaminovorans)
- Smods-associated and fused to various effectors domain-containing protein (63 kDa, Protein from Candidatus Cloacimonas acidaminovorans)
- Ca4 (Complex from synthetic construct)
Cryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4>p
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 9eyk
Q-score: 0.466
Smalakyte D, Ruksenaite A, Sasnauskas G, Tamulaitiene G, Tamulaitis G
Mol Cell (2024) 84 pp. 4239-4255.e8 [ Pubmed: 39362215 DOI: doi:10.1016/j.molcel.2024.09.002 ]
- Filament fragment of a4>p bound ccacalpl (Complex)
- A4>p (5'-r(*ap*ap*ap*(a23))-3') (1 kDa, RNA from synthetic construct)
- Ccacalpl (Complex from Candidatus Cloacimonas acidaminovorans)
- Smods-associated and fused to various effectors domain-containing protein (63 kDa, Protein from Candidatus Cloacimonas acidaminovorans)
- A4>p (Complex from synthetic construct)
Helical structure of BcThsA in complex with 1''-3'gcADPR
Resolution: 2.96 Å
EM Method: Helical reconstruction
Fitted PDBs: 8bto
Q-score: 0.535
Tamulaitiene G, Sabonis D, Sasnauskas G, Ruksenaite A, Silanskas A, Avraham C, Ofir G, Sorek R, Zaremba M, Siksnys V
Nature (2024) 627 pp. 431-436 [ DOI: doi:10.1038/s41586-024-07092-x Pubmed: 38383786 ]
- Nad(+) hydrolase thsa (55 kDa, Protein from Bacillus cereus MSX-D12)
- (2r,3r,3as,5s,6r,7s,8r,11r,13s,15ar)-2-(6-amino-9h-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2h,5h,11h,13h-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione (541 Da, Ligand)
- Bcthsa in complex with 1''-3'gcadpr (Complex from Bacillus cereus)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Helical structure of BcThsA in complex with 1''-3'gc(etheno)ADPR
Resolution: 2.75 Å
EM Method: Helical reconstruction
Fitted PDBs: 8btp
Q-score: 0.577
Tamulaitiene G, Sabonis D, Sasnauskas G, Ruksenaite A, Silanskas A, Avraham C, Ofir G, Sorek R, Zaremba M, Siksnys V
Nature (2024) 627 pp. 431-436 [ DOI: doi:10.1038/s41586-024-07092-x Pubmed: 38383786 ]
- Nad(+) hydrolase thsa (55 kDa, Protein from Bacillus cereus MSX-D12)
- (1s,3s,4r,5r,7r,15r,16s,17r)-5-imidazo[2,1-f]purin-3-yl-10,12-bis(oxidanyl)-10,12-bis(oxidanylidene)-2,6,9,11,13,18-hexaoxa-10$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{3,7}]octadecane-4,16,17-triol (565 Da, Ligand)
- Bcthsa in complex with 1''-3'gc(etheno)adpr (Complex from Bacillus cereus)
- Etheno-nad (687 Da, Ligand)
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
Cami1-ribosome local refinement map with mask on Cami1 and L12-Cter
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
Cami1-ribosome local refinement map with mask on 30S subunit
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
Cami1-ribosome local refinement map with mask on 50S subunit
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
cA4-bound Cami1 in complex with 70S ribosome
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8phj
Q-score: 0.584
Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas C, Siksnys V, Tamulaitis G
Science (2023) 382 pp. 1036-1041 [ DOI: doi:10.1126/science.adj2107 Pubmed: 38033086 ]
- Synthetic mrna (Complex from synthetic construct)
- Large ribosomal subunit protein bl35 (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl25 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs20 (9 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli)
- Fmet-trna(fmet) (24 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl19 (13 kDa, Protein from Escherichia coli)
- Crispr-associated protein cami1, ape2256 family (Complex from Allochromatium vinosum)
- Zinc ion (65 Da, Ligand)
- Small ribosomal subunit protein bs6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- Cami1 bound in 70s e.coli ribosome (Complex)
- Large ribosomal subunit protein ul23 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul30 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us2 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us13 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul2 (29 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul6 (18 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul4 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl21 (11 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli)
- 70s e.coli ribosome (Complex from Escherichia coli)
- Large ribosomal subunit protein ul14 (13 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us19 (10 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl17 (14 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul29 (7 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs16 (9 kDa, Protein from Escherichia coli)
- Ca4 (Complex from Streptococcus thermophilus)
- Large ribosomal subunit protein bl20 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl28 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul18 (12 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us9 (14 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl31a (7 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul16 (15 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl9 (15 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul22 (12 kDa, Protein from Escherichia coli)
- Crispr-associated protein, ape2256 family (45 kDa, Protein from Allochromatium vinosum)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli)
- 23s rrna (2862-mer) (941 kDa, RNA from Escherichia coli)
- Mrna (10 kDa, RNA from synthetic construct)
- Large ribosomal subunit protein ul10 (17 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl33 (6 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us10 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul13 (16 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul3 (22 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl12 (12 kDa, Protein from Escherichia coli)
- Cyclic tetraadenosine monophosphate (ca4) (1 kDa, RNA from Streptococcus thermophilus)
- Large ribosomal subunit protein bl36a (4 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us14 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein bl32 (6 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul15 (15 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- Large ribosomal subunit protein bl27 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein bl34 (5 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul24 (11 kDa, Protein from Escherichia coli)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli)
- Small ribosomal subunit protein us7 (20 kDa, Protein from Escherichia coli)