Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 9cjh
Q-score: 0.296
Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA
Nucleic Acids Res (2025) 53 [ Pubmed: 39698811 DOI: doi:10.1093/nar/gkae1192 ]
- Grna:dna (Complex from synthetic construct)
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Target dna strand (9 kDa, DNA from synthetic construct)
- Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 1 (185 kDa, Complex)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 9cji
Q-score: 0.316
Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA
Nucleic Acids Res (2025) 53 [ Pubmed: 39698811 DOI: doi:10.1093/nar/gkae1192 ]
- Grna:dna (Complex from synthetic construct)
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Target dna strand (9 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
- Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 2 (185 kDa, Complex)
Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 3
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9cjj
Q-score: 0.324
Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA
Nucleic Acids Res (2024) [ Pubmed: 39698811 DOI: doi:10.1093/nar/gkae1192 ]
- Grna:dna (Complex from synthetic construct)
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Target dna strand (9 kDa, DNA from synthetic construct)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 3 (185 kDa, Complex)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
E.coli PNPase in complex with single 8-oxoG RNA
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8vah
Q-score: 0.426
Miller LG, Kim W, Schowe S, Taylor K, Han R, Jain V, Park R, Sherman M, Fang J, Ramirez H, Ellington A, Tamamis P, Resendiz MJE, Zhang YJ, Contreras L
PNAS (2024) 121 pp. e2317865121-e2317865121 [ Pubmed: 39495922 DOI: doi:10.1073/pnas.2317865121 ]
- Rna (5'-r(p*ap*ap*ap*ap*ap*ap*a*a*a)-3') (2 kDa, RNA from Escherichia coli)
- Rna (5'-r(p*ap*cp*ap*(8gm))-3') (1 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Pnpase complexed with single 8-oxo g rna (Complex from Escherichia coli)
- Polyribonucleotide nucleotidyltransferase (77 kDa, Protein from Escherichia coli)
E.coli PNPase in complex with double 8-oxoG RNA
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8vak
Q-score: 0.413
Miller LG, Kim W, Schowe S, Taylor K, Han R, Jain V, Park R, Sherman M, Fang J, Ramirez H, Ellington A, Tamamis P, Resendiz MJE, Zhang YJ, Contreras L
PNAS (2024) 121 pp. e2317865121-e2317865121 [ Pubmed: 39495922 DOI: doi:10.1073/pnas.2317865121 ]
- Rna (5'-r(p*ap*ap*ap*ap*ap*ap*a*a*a)-3') (2 kDa, RNA from Escherichia coli)
- Rna (5'-r(p*cp*ap*(8gm)p*(8gm))-3') (1 kDa, RNA from Escherichia coli)
- Pnpase complexed with double 8-oxo g rna (Complex from Escherichia coli)
- Polyribonucleotide nucleotidyltransferase (77 kDa, Protein from Escherichia coli)
Cryo-EM structure of the tetrameric SPARSA gRNA-ssDNA complex
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 8y80
Q-score: 0.331
Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N
Nat Commun (2024) 15 pp. 8610-8610 [ DOI: doi:10.1038/s41467-024-52910-5 Pubmed: 39366953 ]
- Magnesium ion (24 Da, Ligand)
- Rna (21-mer) (6 kDa, RNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Tetrameric sparsa grna-ssdna complex (Complex from Geobacter sulfurreducens)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
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 [ Pubmed: 38844755 DOI: doi:10.1038/s41467-024-49271-4 ]
- Magnesium ion (24 Da, Ligand)
- 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)
- Water (18 Da, Ligand)
- 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)
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Sparta complex with grna/tdna (Complex from Thermoflavifilum thermophilum)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
SpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loop
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8t79
Q-score: 0.383
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 ]
- Ternary complex of spry-cas9 with grna and non-target dna with 10 bp r-loop (211 kDa, Complex from Streptococcus pyogenes)
- Grna (28 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Nts (2 kDa, DNA from Escherichia phage Lambda)
- Ts (6 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex targeting TGG PAM DNA
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8spq
Q-score: 0.431
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 ]
- Ts (5 kDa, DNA from Escherichia phage Lambda)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna (211 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes serotype M1)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Nts (5 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex targeting TTC PAM DNA
Resolution: 3.69 Å
EM Method: Single-particle
Fitted PDBs: 8sqh
Q-score: 0.379
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 ]
- Ts (5 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Ts (4 kDa, DNA from Escherichia phage Lambda)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna oligo (211 kDa, Complex from Streptococcus pyogenes)