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 ]
- Dimer complex (Complex from Escherichia coli)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Retinal (284 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Heliorhodopsin (28 kDa, Protein from Escherichia coli)
- Nanobody b4 (13 kDa, Protein from Vicugna pacos)
- 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)
- Nicotinamide (122 Da, Ligand)
- Retron ec86-effector fiber (Complex 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)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein 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)
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 ]
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex 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 h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA 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 ]
- 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)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 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)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h4 (9 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 ]
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 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)
- 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)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Histone h4 (9 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 [ DOI: doi:10.1038/s41467-024-48601-w Pubmed: 38773072 ]
- Heavy chain of 1e5 fab fragments (26 kDa, Protein from Macaca mulatta)
- Glycoprotein g (56 kDa, Protein from Nipah virus)
- Cryo-em structure of conformation 1 of complex of nipah virus attachment glycoprotein g with 1e5 neutralizing antibody (Complex from Nipah virus)
- Light chain of 1e5 fab fragments (23 kDa, Protein from Macaca mulatta)
- Glycoprotein g (6 kDa, Protein 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 [ DOI: doi:10.1038/s41467-024-48601-w Pubmed: 38773072 ]
- Cryo-em structure of conformation 2 of complex of nipah virus attachment g with 1e5 neutralizing antibody (Complex from Nipah virus)
- The light chain of 1e5 (23 kDa, Protein from Macaca mulatta)
- Glycoprotein g (45 kDa, Protein from Nipah virus)
- The heavy chain of 1e5 (26 kDa, Protein from Macaca mulatta)