Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens (UltrAuFoil)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8hsb
Q-score: 0.38
Yan Y, Xiao J, Huang F, Xian W, Yu B, Cheng R, Wu H, Lu X, Wang X, Huang W, Li J, Oyejobi GK, Robinson CV, Wu H, Wu D, Liu X, Wang L, Zhu B
Nat Microbiol (2024) 9 pp. 1566-1578 [ Pubmed: 38649411 DOI: doi:10.1038/s41564-024-01684-z ]
- Cdng (45 kDa, Protein from Serratia marcescens)
- Cdng-e2 binary complex (Complex from Serratia marcescens)
- Type vi secretion protein (18 kDa, Protein from Serratia marcescens)
Cryo-EM Structure of CdnG-E2 complex from Serratia marcescens
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8yjy
Q-score: 0.426
Yan Y, Xiao J, Huang F, Xian W, Yu B, Cheng R, Wu H, Lu X, Wang X, Huang W, Li J, Oyejobi GK, Robinson CV, Wu H, Wu D, Liu X, Wang L, Zhu B
Nat Microbiol (2024) 9 pp. 1566-1578 [ Pubmed: 38649411 DOI: doi:10.1038/s41564-024-01684-z ]
- Cdng-e2 binary complex (Complex from Serratia marcescens)
- Type vi secretion protein (18 kDa, Protein from Serratia marcescens)
- Smcdng (45 kDa, Protein from Serratia marcescens)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8jq9
Q-score: 0.556
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus (strain VD045))
- Gaja (276 kDa, Complex from Bacillus cereus (strain VD045))
Structure of Gabija GajA-GajB 4:4 Complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8jqb
Q-score: 0.377
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus VD045)
- Gabija protein gajb (57 kDa, Protein from Bacillus cereus VD045)
- Gaja-gajb 4:4 complex (512 kDa, Complex from Bacillus cereus VD045)
Structure of Gabija GajA-GajB 4:1 complex
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8jqc
Q-score: 0.426
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus (strain VD045))
- 4:1 gajab complex (335 kDa, Complex from Bacillus cereus (strain VD045))
- Gabija protein gajb (57 kDa, Protein from Bacillus cereus (strain VD045))
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 8wy4
Q-score: 0.505
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Endonuclease gaja (66 kDa, Protein from Bacillus cereus VD045)
- Gaja tetramer with atp (Complex from Bacillus cereus VD045)
Structure of Gabija GajA in complex with DNA
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8wy5
Q-score: 0.414
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Calcium ion (40 Da, Ligand)
- Dna (5'-d(p*ap*ap*ap*ap*tp*ap*ap*cp*cp*gp*gp*gp*tp*tp*ap*tp*tp*ap*a)-3') (5 kDa, DNA from synthetic construct)
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus VD045)
- Binary complex of gaja with dsdna (Complex from Bacillus cereus VD045)
- Dna (5'-d(p*tp*tp*ap*ap*tp*ap*ap*cp*cp*cp*gp*gp*tp*tp*ap*tp*tp*tp*t)-3') (5 kDa, DNA from synthetic construct)
Structure of DNA-bound GajA dimer (focused refinement)
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 8x51
Q-score: 0.494
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Calcium ion (40 Da, Ligand)
- Dna (5'-d(*tp*tp*tp*ap*ap*tp*ap*ap*cp*cp*cp*gp*gp*tp*tp*ap*tp*tp*tp*tp*t)-3') (6 kDa, DNA from synthetic construct)
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus VD045)
- Dna (5'-d(*ap*ap*ap*ap*ap*tp*ap*ap*cp*cp*gp*gp*gp*tp*tp*ap*tp*tp*ap*ap*a)-3') (6 kDa, DNA from synthetic construct)
- Binary complex of gaja with dsdna (Complex from Bacillus cereus VD045)
Structure of ATP/Mg2+ bound Gabija GajA
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8x5i
Q-score: 0.515
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus VD045)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Binary complex of gabija with atp (Complex from Bacillus cereus VD045)
- Magnesium ion (24 Da, Ligand)
Structure of ATP/Mg2+ bound Gabija GajA-GajB 4:4 complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8x5n
Q-score: 0.487
Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L
Nature (2024) 629 pp. 467-473 [ Pubmed: 38471529 DOI: doi:10.1038/s41586-024-07270-x ]
- Gaja tetramer with four gajb(atp binding state) (Complex from Bacillus cereus VD045)
- Endonuclease gaja (67 kDa, Protein from Bacillus cereus VD045)
- Gabija protein gajb (57 kDa, Protein from Bacillus cereus VD045)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)