cryo-EM structure of a nanobody bound heliorhodopsin
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 9ljj
Q-score: 0.531
Xia R, Sun M, Lu Y, Wang N, Zhang A, Guo C, Xu Z, Cai X, He Y
Biochem Biophys Res Commun (2025) 750 pp. 151398-151398 [ Pubmed: 39889627 DOI: doi:10.1016/j.bbrc.2025.151398 ]
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Nanobody b4 (13 kDa, Protein from Vicugna pacos)
- Heliorhodopsin (28 kDa, Protein from Escherichia coli)
- Retinal (284 Da, Ligand)
- Dimer complex (Complex from Escherichia coli)
- Acetate ion (59 Da, Ligand)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9jm0
Q-score: 0.492
Wang Y, Wang C, Guan Z, Cao J, Xu J, Wang S, Cui Y, Wang Q, Chen Y, Yin Y, Zhang D, Liu H, Sun M, Jin S, Tao P, Zou T
Cell Rep (2024) 43 pp. 114857-114857 [ Pubmed: 39395169 DOI: doi:10.1016/j.celrep.2024.114857 ]
- Rna (82-mer) (26 kDa, RNA from Escherichia coli)
- Rna (5'-r(p*cp*gp*up*ap*ap*gp*gp*gp*up*gp*cp*gp*cp*a)-3') (4 kDa, RNA from Escherichia coli)
- Nicotinamide (122 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- Retron ec86-effector fiber (Complex from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein from Escherichia coli)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7i
Q-score: 0.443
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8x7j
Q-score: 0.391
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7k
Q-score: 0.423
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Cryo-em structures of rnf168/ubch5c-ub in complex with h2ak13ub nucleosomes determined by activity-based chemical trapping strategy (adjacent h2ak13/15 dual-monoubiquitination) (Complex from Homo sapiens)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8k0c
Q-score: 0.397
Fan P, Sun M, Zhang X, Zhang H, Liu Y, Yao Y, Li M, Fang T, Sun B, Chen Z, Chi X, Chen L, Peng C, Chen Z, Zhang G, Ren Y, Liu Z, Li Y, Li J, Li E, Guan W, Li S, Gong R, Zhang K, Yu C, Chiu S
Nat Commun (2024) 15 pp. 4330-4330 [ Pubmed: 38773072 DOI: doi:10.1038/s41467-024-48601-w ]
- Glycoprotein g (56 kDa, Protein from Nipah virus)
- Light chain of 1e5 fab fragments (23 kDa, Protein from Macaca mulatta)
- Glycoprotein g (6 kDa, Protein from Nipah virus)
- Heavy chain of 1e5 fab fragments (26 kDa, Protein from Macaca mulatta)
- Cryo-em structure of conformation 1 of complex of nipah virus attachment glycoprotein g with 1e5 neutralizing antibody (Complex from Nipah virus)
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 8k0d
Q-score: 0.461
Fan P, Sun M, Zhang X, Zhang H, Liu Y, Yao Y, Li M, Fang T, Sun B, Chen Z, Chi X, Chen L, Peng C, Chen Z, Zhang G, Ren Y, Liu Z, Li Y, Li J, Li E, Guan W, Li S, Gong R, Zhang K, Yu C, Chiu S
Nat Commun (2024) 15 pp. 4330-4330 [ Pubmed: 38773072 DOI: doi:10.1038/s41467-024-48601-w ]
- Cryo-em structure of conformation 2 of complex of nipah virus attachment g with 1e5 neutralizing antibody (Complex from Nipah virus)
- Glycoprotein g (45 kDa, Protein from Nipah virus)
- The light chain of 1e5 (23 kDa, Protein from Macaca mulatta)
- The heavy chain of 1e5 (26 kDa, Protein from Macaca mulatta)