Cryo-EM structure of partial VP4 from simian rotavirus SA11
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 8ygr
Q-score: 0.413
Huang Y, Song F, Zeng Y, Sun H, Sheng R, Wang X, Liu L, Luo G, Jiang Y, Chen Y, Zhang M, Zhang S, Gu Y, Yu H, Li S, Li T, Zheng Q, Ge S, Zhang J, Xia N
Nat Commun (2025) 16 pp. 838-838 [ Pubmed: 39833145 DOI: doi:10.1038/s41467-025-56114-3 ]
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
- Rotavirus a (Virus from Rotavirus A)
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
- Partial vp4 of rotavirus (Complex from Rotavirus A)
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8ygs
Q-score: 0.444
Huang Y, Song F, Zeng Y, Sun H, Sheng R, Wang X, Liu L, Luo G, Jiang Y, Chen Y, Zhang M, Zhang S, Gu Y, Yu H, Li S, Li T, Zheng Q, Ge S, Zhang J, Xia N
Nat Commun (2025) 16 pp. 838-838 [ Pubmed: 39833145 DOI: doi:10.1038/s41467-025-56114-3 ]
- Antibody 7h13 heavy chain (12 kDa, Protein from Mus musculus)
- Rotavirus vp4 (Complex from Rotavirus A)
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
- Fab 7h13 (Complex from Mus musculus)
- Immune complex of rotavirus with 7h13 (Complex from Rotavirus A)
- Antibody 7h13 light chain (11 kDa, Protein from Mus musculus)
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13-I54G mutant (left side)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8ygt
Q-score: 0.559
Huang Y, Song F, Zeng Y, Sun H, Sheng R, Wang X, Liu L, Luo G, Jiang Y, Chen Y, Zhang M, Zhang S, Gu Y, Yu H, Li S, Li T, Zheng Q, Ge S, Zhang J, Xia N
Nat Commun (2025) 16 pp. 838-838 [ Pubmed: 39833145 DOI: doi:10.1038/s41467-025-56114-3 ]
- Rotavirus vp4 (Complex from Rotavirus A)
- Fab 7h13 (Complex from Mus musculus)
- Antibody 7h13-i54g mutant light chain (11 kDa, Protein from Mus musculus)
- Antibody 7h13-i54g mutant heavy chain (12 kDa, Protein from Mus musculus)
- Immune complex of rotavirus with 7h13 (Complex from Rotavirus A)
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
Cryo-EM structure of simian rotavirus SA11 VP4 in complex with nAb 7H13-I54G mutant (right side)
Resolution: 3.13 Å
EM Method: Single-particle
Fitted PDBs: 8ygu
Q-score: 0.526
Huang Y, Song F, Zeng Y, Sun H, Sheng R, Wang X, Liu L, Luo G, Jiang Y, Chen Y, Zhang M, Zhang S, Gu Y, Yu H, Li S, Li T, Zheng Q, Ge S, Zhang J, Xia N
Nat Commun (2025) 16 pp. 838-838 [ Pubmed: 39833145 DOI: doi:10.1038/s41467-025-56114-3 ]
- Outer capsid protein vp4 (64 kDa, Protein from Rotavirus A)
- Antibody 7h13-i54g mutant light chain (11 kDa, Protein from Mus musculus)
- Outer capsid protein vp4 (87 kDa, Protein from Rotavirus A)
- Antibody 7h13-i54g mutant heavy chain (12 kDa, Protein from Mus musculus)
- Immune complex of rotavirus with 7h13-i54g mutant (Complex from Rotavirus A)
- Fab 7h13 (Complex from Rotavirus A)
- Rotavirus vp4 (Complex from Rotavirus A)
Structure of the extracellular domain of Protein Sevenless
Resolution: 3.94 Å
EM Method: Single-particle
Fitted PDBs: 9bhx
Q-score: 0.36
Zhang J, Tsutsui Y, Li H, Li T, Wang Y, Laraki S, Alarcon-Frias S, Stayrook SE, Klein DE
Nat Commun (2025) 16 pp. 808-808 [ Pubmed: 39827240 DOI: doi:10.1038/s41467-025-55943-6 ]
- Protein sevenless (181 kDa, Protein from Drosophila melanogaster)
- Protein sevenless (Cell from Drosophila melanogaster)
Integrin alpha-v beta-8 in complex with the Fab of 130H2
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9ind
Q-score: 0.533
Guo C, Sun H, Du Y, Dai X, Pang Y, Han Z, Xiong X, Li S, Zhang J, Zheng Q, Gui X
J Exp Clin Cancer Res (2025) 44 pp. 1-1 [ Pubmed: 39743547 DOI: doi:10.1186/s13046-024-03250-1 ]
- The light chain of 130h2-fab (11 kDa, Protein from Mus musculus)
- Integrin alpha-v heavy chain (47 kDa, Protein from Homo sapiens)
- Integrin beta-8 (39 kDa, Protein from Homo sapiens)
- The heavy chain of 130h2-fab (13 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Integrin alpha-v beta-8 (Complex from Homo)
- Integrin alpha-v beta-8 complexed with antibody fab fragment of 130h2 (Complex)
- 130h2-fab (Complex from Mus musculus)
CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8xko
Q-score: 0.486
Jia X, Jing X, Li M, Gao M, Zhong Y, Li E, Liu Y, Li R, Yao G, Liu Q, Zhou M, Hou Y, An L, Hong Y, Li S, Zhang J, Wang W, Zhang K, Gong P, Chiu S
Nat Commun (2024) 15 pp. 10750-10750 [ Pubmed: 39737930 DOI: doi:10.1038/s41467-024-54918-3 ]
- [[(2~{r},3~{r},4~{s},5~{r})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (633 Da, Ligand)
- Rna (5'-r(p*up*up*cp*ap*up*gp*cp*up*ap*cp*gp*cp*gp*up*ap*g)-3') (5 kDa, RNA from synthetic construct)
- Non-structural protein 8 (23 kDa, Protein from Severe acute respiratory syndrome coronavirus)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*cp*up*ap*cp*gp*cp*gp*up*ap*gp*cp*ap*up*g)-3') (4 kDa, RNA from synthetic construct)
- Cryoem structure of compound hnc-1644 bound with rdrp-rna (150 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Rna-directed rna polymerase nsp12 (108 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 7 (10 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8xpo
Q-score: 0.554
Jia X, Jing X, Li M, Gao M, Zhong Y, Li E, Liu Y, Li R, Yao G, Liu Q, Zhou M, Hou Y, An L, Hong Y, Li S, Zhang J, Wang W, Zhang K, Gong P, Chiu S
Nat Commun (2024) 15 pp. 10750-10750 [ Pubmed: 39737930 DOI: doi:10.1038/s41467-024-54918-3 ]
- Rna (14-mer) (4 kDa, RNA from synthetic construct)
- [[(2~{r},3~{r},4~{s},5~{r})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (633 Da, Ligand)
- Lassa virus l protein (Complex from Lassa virus Josiah)
- Rna-directed rna polymerase l (255 kDa, Protein from Lassa virus Josiah)
- Lassa virus rdrp elongation complex with the ntp form of compound 13b bound in the active site (270 kDa, Complex)
- Rna (32-mer) (10 kDa, RNA from synthetic construct)
- Rna (Complex from synthetic construct)
- Rna (9-mer) (2 kDa, RNA from synthetic construct)
The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis
Resolution: 1.85 Å
EM Method: Single-particle
Fitted PDBs: 8uem
Q-score: 0.777
Kropp A, Gillett DL, Venugopal H, Gonzalvez MA, Lingford JP, Jain S, Barlow CK, Zhang J, Greening C, Grinter R
Nat Chem Biol (2025) [ DOI: doi:10.1038/s41589-025-01836-0 Pubmed: 39881213 ]
- [2fe-2s] binding domain protein (17 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Carbon monoxide dehydrogenase (large chain), coxl (85 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cu(i)-s-mo(iv)(=o)oh cluster (224 Da, Ligand)
- Carbon monoxide dehydrogenase medium chain (31 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mocu carbon monoxide dehydrogenase (mocu-codh) (270 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Water (18 Da, Ligand)
- Pterin cytosine dinucleotide (696 Da, Ligand)
Complex of FMDV O/18074 and inter-serotype broadly neutralizing antibodies pOA-2
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 8y0q
Q-score: 0.621
Li F, Wu S, Lv L, Huang S, Zhang Z, Zerang Z, Li P, Cao Y, Bao H, Sun P, Bai X, He Y, Fu Y, Yuan H, Ma X, Zhao Z, Zhang J, Wang J, Wang T, Li D, Zhang Q, He J, Liu Z, Lu Z, Lei D, Li K
PLoS Pathog (2024) 20 pp. e1012623-e1012623 [ DOI: doi:10.1371/journal.ppat.1012623 Pubmed: 39405339 ]
- Poa2 vh (13 kDa, Protein from Sus scrofa)
- Poa2 vl (11 kDa, Protein from Sus scrofa)
- Vp1 of capsid protein (23 kDa, Protein from Foot-and-mouth disease virus O)
- Complex of fmdv o/18074 and inter-serotype broadly neutralizing antibodies poa-2 (Complex)
- Inter-serotype broadly neutralizing antibodies poa-2 (Complex from Sus scrofa)
- Fmdv o/18074 (Complex from Foot-and-mouth disease virus O)
- Vp3 of capsid protein (23 kDa, Protein from Foot-and-mouth disease virus O)
- Vp2 of capsid protein (24 kDa, Protein from Foot-and-mouth disease virus O)
- Vp4 of capsid protein (8 kDa, Protein from Foot-and-mouth disease virus O)