cryo-EM structure of a nanobody bound heliorhodopsin
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 [ DOI: doi:10.1016/j.bbrc.2025.151398 Pubmed: 39889627 ]
- Nanobody b4 (13 kDa, Protein from Vicugna pacos)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Heliorhodopsin (28 kDa, Protein from Escherichia coli)
- Palmitic acid (256 Da, Ligand)
- 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 [ DOI: doi:10.1016/j.celrep.2024.114857 Pubmed: 39395169 ]
- 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)
- Rna (82-mer) (26 kDa, RNA from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein from Escherichia coli)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- Nicotinamide (122 Da, Ligand)
- 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 h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA 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)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein 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)
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 h4 (9 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Ubiquitin (8 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)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 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 h4 (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA from Homo sapiens)
- Histone h3.2 (11 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)
- 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)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 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 ]
- Cryo-em structure of conformation 1 of complex of nipah virus attachment glycoprotein g with 1e5 neutralizing antibody (Complex from Nipah virus)
- Glycoprotein g (6 kDa, Protein from Nipah virus)
- Heavy chain of 1e5 fab fragments (26 kDa, Protein from Macaca mulatta)
- Light chain of 1e5 fab fragments (23 kDa, Protein from Macaca mulatta)
- Glycoprotein g (56 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 [ 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)
- 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)
Nipah virus Attachment glycoprotein with 41-6 antibody fragment
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 8k3c
Q-score: 0.44
Chen L, Sun M, Zhang H, Zhang X, Yao Y, Li M, Li K, Fan P, Zhang H, Qin Y, Zhang Z, Li E, Chen Z, Guan W, Li S, Yu C, Zhang K, Gong R, Chiu S
Nat Commun (2024) 15 pp. 2987-2987 [ Pubmed: 38582870 DOI: doi:10.1038/s41467-024-47213-8 ]
- Glycoprotein g (52 kDa, Protein from Henipavirus nipahense)
- Light chain of 41-6 fab fragment (22 kDa, Protein from Homo sapiens)
- Cryo-em structure of complex of attachment glycoprotein g with 41-6 fab fragment (Complex from Henipavirus nipahense)
- Heavy chain of 41-6 fab fragments (25 kDa, Protein from Homo sapiens)
Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8hqy
Q-score: 0.47
Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L
Nat Struct Mol Biol (2024) 31 pp. 300-310 [ DOI: doi:10.1038/s41594-023-01141-1 Pubmed: 38177667 ]
- Polyubiquitin-b (fragment) (8 kDa, Protein from Homo sapiens)
- Ssx1-h2ak119ub nucleosome complex (290 kDa, Complex from Homo sapiens)
- Dna (136-mer) (42 kDa, DNA from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Protein ssx2 (2 kDa, Protein from Homo sapiens)
- Dna (137-mer) (41 kDa, DNA 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 h4 (fragment) (9 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)