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)
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 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)
SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 18 bp R-loop
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8t6x
Q-score: 0.412
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 ]
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Ternary complex of spry-cas9 with grna and nac pam dna after one minute of dna incubation with 13 bp r-loop (211 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
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 ]
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Water (18 Da, Ligand)
- Dna-mediated dimer of spry-cas9 ternary complexes each with grna (423 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
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 ]
- The complex of protein with grna and target dna (Complex from Firmicutes bacterium AM43-11BH)
- 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)
- Transposase (44 kDa, Protein 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)
- Zinc ion (65 Da, Ligand)
- Rna (207-mer) (66 kDa, RNA from Firmicutes bacterium AM43-11BH)
Symmetric dimer of MapSPARTA bound with gRNA/tDNA hybrid
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8sp0
Q-score: 0.33
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
- Magnesium ion (24 Da, Ligand)
- Guide rna (6 kDa, RNA from synthetic construct)
- Symmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Target dna (7 kDa, DNA from synthetic construct)
Asymmetric dimer of MapSPARTA bound with gRNA/tDNA hybrid
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8sp3
Q-score: 0.298
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
- Magnesium ion (24 Da, Ligand)
- Asymmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Target dna (7 kDa, DNA from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Guide rna (6 kDa, RNA from Maribacter polysiphoniae)