Cryo-EM structure of CasLambda (Cas12l) bound to crRNA and DNA
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8dc2
Q-score: 0.491
Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA
Cell (2022) 185 pp. 4574-4586.e16 [ Pubmed: 36423580 DOI: doi:10.1016/j.cell.2022.10.020 ]
- Dna ts (14 kDa, DNA from uncultured virus)
- Caslambda-crrna-dsdna ternary structure (Complex from uncultured virus)
- Dna nts (14 kDa, DNA from uncultured virus)
- Rna (51-mer) (16 kDa, RNA from uncultured virus)
- Caslambda (87 kDa, Protein from uncultured virus)
CryoEM structure of type III-E CRISPR gRAMP-crRNA binary complex
Resolution: 2.71 Å
EM Method: Single-particle
Fitted PDBs: 7y80
Q-score: 0.562
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Type iii-e crispr gramp-crrna binary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp (Complex from Candidatus Scalindua brodae)
- Crrna (Complex)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
CryoEM structure of type III-E CRISPR gRAMP-crRNA complex bound to non-self RNA target
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 7y81
Q-score: 0.607
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Non-self rna target (Complex)
- Type iii-e crispr gramp-crrna binary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp (Complex from Candidatus Scalindua brodae)
- Crrna (Complex)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
- Non-self rna target (18 kDa, RNA from Candidatus Scalindua brodae)
CryoEM structure of type III-E CRISPR gRAMP-crRNA complex bound to self RNA target
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 7y82
Q-score: 0.551
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Self rna target (Complex)
- Type iii-e crispr gramp-crrna binary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp (Complex from Candidatus Scalindua brodae)
- Crrna (Complex)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
- Self rna target (18 kDa, RNA from Candidatus Scalindua brodae)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 7y83
Q-score: 0.53
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Type iii-e crispr gramp-crrna binary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp (Complex from Candidatus Scalindua brodae)
- Crrna (Complex)
- Non-self rna (18 kDa, RNA from Candidatus Scalindua brodae)
- Tpr-chat (Complex)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (85 kDa, Protein from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
- Non-self rna target (Complex from Candidatus Scalindua brodae)
CryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with TPR-CHAT
Resolution: 2.61 Å
EM Method: Single-particle
Fitted PDBs: 7y84
Q-score: 0.614
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Crrna (Complex)
- Type iii-e crispr gramp-crrna in complex with tpr-chat (Complex from Candidatus Scalindua brodae)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein/chat (Complex from Candidatus Scalindua brodae)
- Chat domain protein (85 kDa, Protein from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
CryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with TPR-CHAT bound to self RNA target
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 7y85
Q-score: 0.57
Cui N, Zhang JT, Li Z, Liu XY, Wang C, Huang H, Jia N
Nat Commun (2022) 13 pp. 7549-7549 [ Pubmed: 36477448 DOI: doi:10.1038/s41467-022-35275-5 ]
- Type iii-e crispr gramp-crrna binary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (198 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Gramp (Complex from Candidatus Scalindua brodae)
- Crrna (Complex)
- Self rna target (Complex from Candidatus Scalindua brodae)
- Tpr-chat (Complex)
- Crrna (35 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (85 kDa, Protein from Candidatus Scalindua brodae)
- Magnesium ion (24 Da, Ligand)
- Self rna target (18 kDa, RNA from Candidatus Scalindua brodae)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8e56
Q-score: 0.54
Yao X, Gao S, Wang J, Li Z, Huang J, Wang Y, Wang Z, Chen J, Fan X, Wang W, Jin X, Pan X, Yu Y, Lagrutta A, Yan N
Cell (2022) 185 pp. 4801-4810.e13 [ Pubmed: 36417914 DOI: doi:10.1016/j.cell.2022.10.024 ]
- (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone (645 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Voltage-dependent calcium channel gamma-1 subunit (25 kDa, Protein from Oryctolagus cuniculus)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (125 kDa, Protein from Oryctolagus cuniculus)
- Cav1.1 (Complex from Oryctolagus cuniculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Voltage-dependent l-type calcium channel subunit alpha-1s (212 kDa, Protein from Oryctolagus cuniculus)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8e57
Q-score: 0.534
Yao X, Gao S, Wang J, Li Z, Huang J, Wang Y, Wang Z, Chen J, Fan X, Wang W, Jin X, Pan X, Yu Y, Lagrutta A, Yan N
Cell (2022) 185 pp. 4801-4810.e13 [ Pubmed: 36417914 DOI: doi:10.1016/j.cell.2022.10.024 ]
- (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone (645 Da, Ligand)
- Propan-2-yl (2s)-2-{[(s)-{[(2r,3s,4r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name) (535 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Voltage-dependent calcium channel gamma-1 subunit (25 kDa, Protein from Oryctolagus cuniculus)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (125 kDa, Protein from Oryctolagus cuniculus)
- Cav1.1 (Complex from Oryctolagus cuniculus)
- Voltage-dependent l-type calcium channel subunit alpha-1s (212 kDa, Protein from Oryctolagus cuniculus)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8e58
Q-score: 0.533
Yao X, Gao S, Wang J, Li Z, Huang J, Wang Y, Wang Z, Chen J, Fan X, Wang W, Jin X, Pan X, Yu Y, Lagrutta A, Yan N
Cell (2022) 185 pp. 4801-4810.e13 [ Pubmed: 36417914 DOI: doi:10.1016/j.cell.2022.10.024 ]
- (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone (645 Da, Ligand)
- Propan-2-yl (2s)-2-{[(s)-{[(2r,3s,4r,5r)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name) (535 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Voltage-dependent calcium channel gamma-1 subunit (25 kDa, Protein from Oryctolagus cuniculus)
- Voltage-dependent calcium channel subunit alpha-2/delta-1 (125 kDa, Protein from Oryctolagus cuniculus)
- Cav1.1 (Complex from Oryctolagus cuniculus)
- Voltage-dependent l-type calcium channel subunit alpha-1s (212 kDa, Protein from Oryctolagus cuniculus)