Cryo-EM structure of the prokaryotic SPARSA system complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8jkz
Q-score: 0.475
Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S
Nat Commun (2024) 15 pp. 450-450 [ Pubmed: 38200015 DOI: doi:10.1038/s41467-023-44660-7 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Sir2/ago (Complex from Geobacter sulfurreducens PCA)
- Ago (Complex)
- Sir2 (Complex from Geobacter sulfurreducens PCA)
Cryo-EM structure of the prokaryotic SPARSA system complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8jl0
Q-score: 0.547
Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S
Nat Commun (2024) 15 pp. 450-450 [ Pubmed: 38200015 DOI: doi:10.1038/s41467-023-44660-7 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- The sir2/ago/guide rna/recognition dna complex (Complex from Geobacter sulfurreducens PCA)
- Dna/guide rna duplex (Complex)
- Rna (5'-r(p*ap*up*ap*ap*up*gp*gp*up*up*up*cp*up*up*ap*gp*ap*cp*gp*up*cp*gp*u)-3') (6 kDa, RNA from synthetic construct)
- Ago (Complex)
- Dna (5'-d(p*ap*cp*gp*ap*cp*gp*tp*cp*tp*ap*ap*gp*ap*ap*ap*cp*cp*ap*tp*tp*ap*t)-3') (6 kDa, DNA from synthetic construct)
- Sir2 (Complex from Geobacter sulfurreducens PCA)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
Cryo-EM structure of the target ssDNA-bound SIR2-APAZ/Ago-gRNA quaternary complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8in8
Q-score: 0.504
Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H
Cell Res (2023) 33 pp. 699-711 [ DOI: doi:10.1038/s41422-023-00839-7 Pubmed: 37311833 ]
- Dna (5'-d(p*ap*ap*cp*gp*ap*cp*gp*tp*cp*tp*ap*ap*gp*ap*ap*ap*cp*cp*ap*tp*tp*ap*a)-3') (7 kDa, DNA from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Cryo-em structure of the target ssdna-bound sir2-apaz/ago-grna quaternary complex (Complex from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Rna (5'-r(p*ap*up*ap*ap*up*gp*gp*up*up*up*cp*up*up*ap*gp*ap*cp*gp*up*cp*gp*up*up*u)-3') (7 kDa, RNA from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Magnesium ion (24 Da, Ligand)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Cryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens
Resolution: 3.4 Å
EM Method: Helical reconstruction
Fitted PDBs: 7lq5
Q-score: 0.462
Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS
Nat Microbiol (2023) 8 pp. 284-298 [ Pubmed: 36732469 DOI: doi:10.1038/s41564-022-01315-5 ]
- Polymerized cytochrome omcz from geobacter sulfurreducens (Complex from Geobacter sulfurreducens)
- Cytochrome c (27 kDa, Protein from Geobacter sulfurreducens PCA)
- Heme c (618 Da, Ligand)
Cascade complex from type I-A CRISPR-Cas system
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7tr6
Q-score: 0.263
Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A
Mol Cell (2022) 82 pp. 2754-2768.e5 [ Pubmed: 35835111 DOI: doi:10.1016/j.molcel.2022.06.007 ]
- Cas5a (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas11a (12 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crrna (45-mer) (14 kDa, RNA from Escherichia coli)
- Cas8a (38 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas7a (36 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cascade complex from pyrococcus furiosus type i-a crispr/cas system (350 kDa, Complex from Geobacter sulfurreducens)
Cascade complex from type I-A CRISPR-Cas system
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7tr8
Q-score: 0.122
Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A
Mol Cell (2022) 82 pp. 2754-2768.e5 [ Pubmed: 35835111 DOI: doi:10.1016/j.molcel.2022.06.007 ]
- Nickel (ii) ion (58 Da, Ligand)
- Cas5a (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas3 bound cascade complex from pyrococcus furiosus type i-a crispr/cas system (400 kDa, Complex from Geobacter sulfurreducens)
- Cas8 (38 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas11a (12 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crispr-associated helicase cas3 (61 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crrna (45-mer) (14 kDa, RNA from Escherichia coli)
- Crispr-associated endonuclease cas3-hd (26 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas7a (36 kDa, Protein from Pyrococcus furiosus DSM 3638)
Cascade complex from type I-A CRISPR-Cas system
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7tr9
Q-score: 0.225
Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A
Mol Cell (2022) 82 pp. 2754-2768.e5 [ Pubmed: 35835111 DOI: doi:10.1016/j.molcel.2022.06.007 ]
- Nickel (ii) ion (58 Da, Ligand)
- Cas5a (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Target strand dna (6 kDa, DNA from Escherichia coli)
- Non-target strand dna (2 kDa, DNA from Escherichia coli)
- Cas11a (12 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crispr-associated helicase cas3 (61 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crrna (45-mer) (14 kDa, RNA from Escherichia coli)
- Crispr-associated endonuclease cas3-hd (26 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas8a (38 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas7a (36 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Partial r-loop state of cas3-cascade complex from pyrococcus furiosus type i-a crispr/cas system (450 kDa, Complex from Geobacter sulfurreducens)
Cascade complex from type I-A CRISPR-Cas system
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7tra
Q-score: 0.324
Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A
Mol Cell (2022) 82 pp. 2754-2768.e5 [ Pubmed: 35835111 DOI: doi:10.1016/j.molcel.2022.06.007 ]
- Full r-loop state of cas3-cascade complex from pyrococcus furiosus type i-a crispr/cas system (450 kDa, Complex from Geobacter sulfurreducens)
- Nickel (ii) ion (58 Da, Ligand)
- Cas5a (29 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas11a (12 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crispr-associated helicase cas3 (61 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crrna (44-mer) (14 kDa, RNA from Escherichia coli)
- Cas8a (38 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Crispr-associated endonuclease cas3-hd (24 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Cas7a (36 kDa, Protein from Pyrococcus furiosus DSM 3638)
- Non-target strand dna (25-mer) (7 kDa, DNA from Escherichia coli)
- Target strand dna (44-mer) (13 kDa, DNA from Escherichia coli)
Symmetrical PAM-PAM prespacer bound Cas4/Cas1/Cas2 complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7mi4
Q-score: 0.492
Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A
Nature (2021) 598 pp. 515-520 [ Pubmed: 34588691 DOI: doi:10.1038/s41586-021-03951-z ]
- Crispr-associated endoribonuclease cas2 (11 kDa, Protein from Geobacter sulfurreducens)
- Crispr-associated exonuclease cas4/endonuclease cas1 fusion (62 kDa, Protein from Geobacter sulfurreducens)
- Dna (35-mer) (10 kDa, DNA from Geobacter sulfurreducens)
- Symmetrical pam-pam prespacer bound cas4/cas1/cas2 complex (300 kDa, Complex from Geobacter sulfurreducens)
- Iron/sulfur cluster (351 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
Asymmetrical PAM-Non PAM prespacer bound Cas4/Cas1/Cas2 complex
Resolution: 3.57 Å
EM Method: Single-particle
Fitted PDBs: 7mi5
Q-score: 0.318
Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A
Nature (2021) 598 pp. 515-520 [ Pubmed: 34588691 DOI: doi:10.1038/s41586-021-03951-z ]
- Crispr-associated endoribonuclease cas2 (11 kDa, Protein from Geobacter sulfurreducens)
- Crispr-associated exonuclease cas4/endonuclease cas1 fusion (62 kDa, Protein from Geobacter sulfurreducens)
- Asymmetrical pam-pam prespacer bound cas4/cas1/cas2 complex (300 kDa, Complex from Geobacter sulfurreducens)
- Dna (26-mer) (11 kDa, DNA from Geobacter sulfurreducens)
- Iron/sulfur cluster (351 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (34-mer) (11 kDa, DNA from Geobacter sulfurreducens)