Cryo-EM structure of the SPARTA oligomer with guide RNA and target DNA
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8u72
Q-score: 0.533
Kottur J, Malik R, Aggarwal AK
Nat Commun (2024) 15 pp. 4852-4852 [ DOI: doi:10.1038/s41467-024-49271-4 Pubmed: 38844755 ]
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Water (18 Da, Ligand)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*a)-3') (6 kDa, RNA from synthetic construct)
- Dna (5'-d(p*tp*ap*tp*ap*cp*ap*ap*cp*cp*tp*ap*cp*tp*ap*cp*cp*tp*c)-3') (13 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Sparta complex with grna/tdna (Complex from Thermoflavifilum thermophilum)
SpRY-Cas9:gRNA complex targeting TAC PAM DNA
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8srs
Q-score: 0.521
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ DOI: doi:10.1038/s41467-024-47830-3 Pubmed: 38688943 ]
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Ts (3 kDa, DNA from Escherichia phage Lambda)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna (211 kDa, Complex from Streptococcus pyogenes)
- Ts (5 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Water (18 Da, Ligand)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8t7s
Q-score: 0.408
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ DOI: doi:10.1038/s41467-024-47830-3 Pubmed: 38688943 ]
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Dna-mediated dimer of spry-cas9 ternary complexes each with grna (423 kDa, Complex from Streptococcus pyogenes)
- Water (18 Da, Ligand)
Cryo-EM structure of the ISFba1 TnpB-reRNA-dsDNA complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8iaz
Q-score: 0.548
Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z
Cell Res (2024) 34 pp. 370-385 [ DOI: doi:10.1038/s41422-024-00952-1 Pubmed: 38575718 ]
- Zinc ion (65 Da, Ligand)
- Dna (5'-d(p*cp*cp*ap*tp*tp*ap*gp*gp*ap*gp*cp*tp*gp*ap*tp*g)-3') (4 kDa, DNA from Firmicutes bacterium AM43-11BH)
- Rna (207-mer) (66 kDa, RNA from Firmicutes bacterium AM43-11BH)
- Dna (5'-d(p*ap*cp*ap*tp*gp*gp*ap*cp*cp*ap*tp*cp*ap*gp*cp*tp*cp*cp*tp*ap*ap*tp*gp*g)-3') (7 kDa, DNA from Firmicutes bacterium AM43-11BH)
- The complex of protein with grna and target dna (Complex from Firmicutes bacterium AM43-11BH)
- Transposase (44 kDa, Protein from Firmicutes bacterium AM43-11BH)
Cryo-EM structure of RNase-untreated RESC-A in trypanosomal RNA editing
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8fn6
Q-score: 0.386
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ Pubmed: 37410820 DOI: doi:10.1126/science.adg4725 ]
- Rna-editing substrate-binding complex protein 3 (resc3) (53 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 1 (resc1) (52 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 4 (resc4) (120 kDa, Protein from Trypanosoma brucei)
- Grna (14 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 2 (resc2) (55 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 5 (resc5) (43 kDa, Protein from Trypanosoma brucei)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 6 (resc6) (57 kDa, Protein from Trypanosoma brucei)
Cryo-EM structure of a CRISPR effector in complex with regulator
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 7zol
Q-score: 0.434
Ekundayo B, Torre D, Beckert B, Nazarov S, Myasnikov A, Stahlberg H, Ni D
Nat Struct Mol Biol (2023) 30 pp. 135-139 [ Pubmed: 36471056 DOI: doi:10.1038/s41594-022-00894-5 ]
- Zinc ion (65 Da, Ligand)
- Tpr-chat (17 kDa, Protein from Desulfonema magnum)
- Cas7-11 (207 kDa, Protein from Desulfonema magnum)
- Cas7-11 with trp-chat-ntd (220 kDa, Complex from Desulfonema magnum)
- Grna (12 kDa, RNA from Desulfonema magnum)
Cas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformation
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7s4x
Q-score: 0.551
Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW
Nature (2022) 603 pp. 343-347 [ DOI: doi:10.1038/s41586-022-04470-1 Pubmed: 35236982 ]
- Ts (4 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Grna (31 kDa, RNA from synthetic construct)
- Ts (6 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Nts (10 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Cas9 bound to 18-20mm dna, 1 min time-point, kinked active conformation (Complex from Streptococcus pyogenes)
Cryo-EM structure of Thermus thermophilus reiterative transcription complex with 11nt oligo-G RNA
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7rdq
Q-score: 0.516
Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH
PNAS (2022) 119 [ Pubmed: 35082149 DOI: doi:10.1073/pnas.2115746119 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Reiterative transcription initiation complex with 11nt oligo-g rna (425 kDa, Complex from Thermus thermophilus HB8)
- Rna polymerase sigma factor siga (48 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta' (170 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Rna (5'-r(p*gp*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (31-mer) nontemplate strand (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Dna (31-mer) template strand (10 kDa, DNA from synthetic construct)