SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA with 1 nucleotide bulge
Resolution: 3.24 Å
EM Method: Single-particle
Fitted PDBs: 9bih
Q-score: 0.266
Wright ZM, Butay KJ, Krahn JM, Wilson IM, Gabel SA, DeRose EF, Hissein IS, Williams JG, Borgnia MJ, Frazier MN, Mueller GA, Stanley RE
Nat Commun (2025) 16 pp. 391-391 [ Pubmed: 39755678 DOI: doi:10.1038/s41467-024-55682-0 ]
- Rna (35-mer) (11 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Uridylate-specific endoribonuclease nsp15 (39 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 endoribonuclease nsp15 bound to dsrna with 1 nucleotide bulge (Complex from Severe acute respiratory syndrome coronavirus 2)
- Rna (34-mer) (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Cryo-EM structure of CTR-bound type VII CRISPR-Cas complex at substrate-engaged state II
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 8z4j
Q-score: 0.507
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ Pubmed: 39143216 DOI: doi:10.1038/s41586-024-07815-0 ]
- Protein structure (27 kDa, Protein from metagenome)
- Protein structure (22 kDa, Protein from metagenome)
- A protein (Complex from metagenome)
- Zinc ion (65 Da, Ligand)
- Rna (38-mer) (19 kDa, RNA from metagenome)
- Protein structure (70 kDa, Protein from metagenome)
- Rna (34-mer) (19 kDa, RNA from metagenome)
Cryo-EM structure of NTR-bound type VII CRISPR-Cas complex at substrate-engaged state II
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8z9e
Q-score: 0.496
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ Pubmed: 39143216 DOI: doi:10.1038/s41586-024-07815-0 ]
- Protein structure (27 kDa, Protein from metagenome)
- Rna (39-mer) (19 kDa, RNA from metagenome)
- Protein structure (Complex from metagenome)
- Protein structure (22 kDa, Protein from metagenome)
- Zinc ion (65 Da, Ligand)
- Protein structure (70 kDa, Protein from metagenome)
- Rna (34-mer) (19 kDa, RNA from metagenome)
WT CRISPR-Cas12a with a 15bp R-loop
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8sfl
Q-score: 0.381
Strohkendl I, Saha A, Moy C, Nguyen AH, Ahsan M, Russell R, Palermo G, Taylor DW
Mol Cell (2024) 84 pp. 2717-2731.e6 [ DOI: doi:10.1016/j.molcel.2024.06.007 Pubmed: 38955179 ]
- Dna (40-mer) (17 kDa, DNA from synthetic construct)
- Rna (34-mer) (15 kDa, RNA from synthetic construct)
- Dna (40-mer) (17 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
- Wt ascas12a incubated with 16bp-complementary target dna (Complex from Acidaminococcus sp. BV3L6)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 7xsq
Q-score: 0.496
Liu X, Zhang L, Wang H, Xiu Y, Huang L, Gao Z, Li N, Li F, Xiong W, Gao T, Zhang Y, Yang M, Feng Y
Mol Cell (2022) 82 pp. 4503-4518.e8 [ DOI: doi:10.1016/j.molcel.2022.10.007 Pubmed: 36306795 ]
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Craspase (Complex from Candidatus Scalindua brodae)
- Rna (34-mer) (23 kDa, RNA from Candidatus Scalindua brodae)
- Rna (Complex)
- Ramp superfamily protein, chat domain protein (Complex from Candidatus Scalindua brodae)
Structure of Craspase-target RNA
Resolution: 2.97 Å
EM Method: Single-particle
Fitted PDBs: 7xsr
Q-score: 0.52
Liu X, Zhang L, Wang H, Xiu Y, Huang L, Gao Z, Li N, Li F, Xiong W, Gao T, Zhang Y, Yang M, Feng Y
Mol Cell (2022) 82 pp. 4503-4518.e8 [ DOI: doi:10.1016/j.molcel.2022.10.007 Pubmed: 36306795 ]
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
- Rna 34-mer (Complex)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Rna (5'-r(p*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*g)-3') (12 kDa, RNA from Candidatus Scalindua brodae)
- Rna (Complex from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Ramp superfamily protein, chat domain protein (Complex)
- Rna (34-mer) (23 kDa, RNA from Candidatus Scalindua brodae)
- Craspase-target rna (Complex from Candidatus Scalindua brodae)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xss
Q-score: 0.465
Liu X, Zhang L, Wang H, Xiu Y, Huang L, Gao Z, Li N, Li F, Xiong W, Gao T, Zhang Y, Yang M, Feng Y
Mol Cell (2022) 82 pp. 4503-4518.e8 [ DOI: doi:10.1016/j.molcel.2022.10.007 Pubmed: 36306795 ]
- Rna (5'-r(p*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*ap*cp*gp*ap*u)-3') (14 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
- Rna 34-mer (Complex)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Craspase-ctr complex (Complex from Candidatus Scalindua brodae)
- Chat domain protein (Complex from Candidatus Scalindua brodae)
- Rna (34-mer) (23 kDa, RNA from Candidatus Scalindua brodae)
- Rna (Complex)
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 7xt4
Q-score: 0.536
Liu X, Zhang L, Wang H, Xiu Y, Huang L, Gao Z, Li N, Li F, Xiong W, Gao T, Zhang Y, Yang M, Feng Y
Mol Cell (2022) 82 pp. 4503-4518.e8 [ DOI: doi:10.1016/j.molcel.2022.10.007 Pubmed: 36306795 ]
- Craspase-ntr complex (Complex from Candidatus Scalindua brodae)
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Rna (Complex from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*gp*up*ap*cp*cp*g)-3') (14 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein, chat domain protein (Complex)
- Rna (34-mer) (17 kDa, RNA from Candidatus Scalindua brodae)
- Rna (34-mer) (Complex)
Cryo-EM structure of guide RNA and target RNA bound Cas7-11
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 8d1v
Q-score: 0.547
Goswami HN, Rai J, Das A, Li H
eLife (2022) 11 [ Pubmed: 36190192 DOI: doi:10.7554/eLife.81678 ]
- Cryoem structure of type iii-e cas7-11 from desulfonema ishimotonii (Complex from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
- Ss target rna (5'-r(p*ap*gp*cp*up*up*gp*gp*up*up*cp*ap*ap*ap*gp*ap*ap*cp*g)-3') (5 kDa, RNA from Desulfonema ishimotonii)
- Crispr rna (34-mer) (10 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (183 kDa, Protein from Desulfonema ishimotonii)
S. cerevisiae spliceosomal post-catalytic P complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6bk8
Q-score: 0.38
Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R
Science (2017) 358 pp. 1278-1283 [ Pubmed: 29146870 DOI: doi:10.1126/science.aar3462 ]
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Lea1 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp8 (279 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp18 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Rna (34-mer) (10 kDa, RNA from Saccharomyces cerevisiae)
- Unknown protein fragment (18 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing factor prp17 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein fragment (1 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Spliceosomal p complex (Complex from Saccharomyces cerevisiae)
- Pre-mrna-processing factor prp19 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Msl1 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rna (59-mer) (18 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inositol hexakisphosphate (660 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))