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 ]
- Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 1 (185 kDa, Complex)
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Grna:dna (Complex from synthetic construct)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
- Target dna strand (9 kDa, DNA from synthetic construct)
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 ]
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Grna:dna (Complex from synthetic construct)
- Crispr-associated endonuclease cas12a (151 kDa, Protein from Acidaminococcus sp. BV3L6)
- Target dna strand (9 kDa, DNA from synthetic construct)
- Cas12a:grna:dna (acidaminococcus sp.) with 0 rna:dna base pairs, structure 2 (185 kDa, Complex)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
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 ]
- Guide rna (25-mer) (13 kDa, RNA from synthetic construct)
- Grna:dna (Complex 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 3 (185 kDa, Complex)
- Cas12a (Complex from Acidaminococcus sp. BV3L6)
- Non-target dna strand (9 kDa, DNA from synthetic construct)
- Target dna strand (9 kDa, DNA from synthetic construct)
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 ]
- Polyribonucleotide nucleotidyltransferase (77 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 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)
- Pnpase complexed with single 8-oxo g rna (Complex 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*cp*ap*(8gm)p*(8gm))-3') (1 kDa, RNA from Escherichia coli)
- Polyribonucleotide nucleotidyltransferase (77 kDa, Protein from Escherichia coli)
- Rna (5'-r(p*ap*ap*ap*ap*ap*ap*a*a*a)-3') (2 kDa, RNA from Escherichia coli)
- Pnpase complexed with double 8-oxo g rna (Complex from Escherichia coli)
Cryo-EM structure of the monomeric SPARSA gRNA-ssDNA complex
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8y7z
Q-score: 0.587
Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N
Nat Commun (2024) 15 pp. 8610-8610 [ Pubmed: 39366953 DOI: doi:10.1038/s41467-024-52910-5 ]
- Monomeric sparsa grna-ssdna complex (Complex from Geobacter sulfurreducens)
- Rna (21-mer) (6 kDa, RNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Magnesium ion (24 Da, Ligand)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
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 [ Pubmed: 39366953 DOI: doi:10.1038/s41467-024-52910-5 ]
- Rna (21-mer) (6 kDa, RNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Dna (25-mer) (7 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Magnesium ion (24 Da, Ligand)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Tetrameric sparsa grna-ssdna complex (Complex from Geobacter sulfurreducens)
Structure of PsCas9 in complex with gRNA and DNA in product state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8umf
Q-score: 0.526
To Be Published
- Pscas9 in with grna and dsdna, product state (211 kDa, Complex from Parasutterella secunda)
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna (121-mer) (41 kDa, RNA from synthetic construct)
- Cas9 (168 kDa, Protein from Parasutterella secunda)
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
Kottur J, Malik R, Aggarwal AK
Nat Commun (2024) 15 pp. 4852-4852 [ DOI: doi:10.1038/s41467-024-49271-4 Pubmed: 38844755 ]
Kottur J, Malik R, Aggarwal AK
Nat Commun (2024) 15 pp. 4852-4852 [ DOI: doi:10.1038/s41467-024-49271-4 Pubmed: 38844755 ]