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)