SARS-CoV-2 S RBD (C.37 Lambda variant) plus S309 Fab, local refinement
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8vyg
Q-score: 0.395
Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB
Nat Commun (2024) 15 pp. 2175-2175 [ Pubmed: 38467646 DOI: doi:10.1038/s41467-024-46536-w ]
- S309 light chain (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s c.37 (lambda variant) plus s309, s2l20, and s2x303 fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- S309 heavy chain (14 kDa, Protein from Homo sapiens)
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8iss
Q-score: 0.497
Yuan L, Han Y, Zhao J, Zhang Y, Sun Y
Nat Commun (2023) 14 pp. 6071-6071 [ DOI: doi:10.1038/s41467-023-41845-y Pubmed: 37770519 ]
- Rna (88-mer) (28 kDa, RNA from Homo sapiens)
- Trna-splicing endonuclease subunit sen34 (33 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Trna-splicing endonuclease subunit sen54 (59 kDa, Protein from Homo sapiens)
- Trna-splicing endonuclease subunit sen15 (19 kDa, Protein from Homo sapiens)
- Trna-splicing endonuclease subunit sen2 (53 kDa, Protein from Homo sapiens)
- Human pre-trna splicing complex tsen with substrate rna (Complex from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.12.1 RBD in complex with human ACE2 (local refinement)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7yhw
Q-score: 0.516
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Zinc ion (65 Da, Ligand)
- Omicron ba.2.12.1 rbd (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of sars-cov-2 omicron ba.2.12.1 rbd in complex with human ace2 (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Ace2 (Complex)
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human ACE2 (local refinement)
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 7yj3
Q-score: 0.468
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Omicron ba.2 rbd (Complex)
- Cryo-em structure of sars-cov-2 omicron ba.2 rbd in complex with human ace2 (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8h06
Q-score: 0.566
Zhao Z, Xie Y, Bai B, Luo C, Zhou J, Li W, Meng Y, Li L, Li D, Li X, Li X, Wang X, Sun J, Xu Z, Sun Y, Zhang W, Fan Z, Zhao X, Wu L, Ma J, Li OY, Shang G, Chai Y, Liu K, Wang P, Gao GF, Qi J
Nat Commun (2023) 14 pp. 4405-4405 [ Pubmed: 37479708 DOI: doi:10.1038/s41467-023-39942-z ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Cryo-em structure of sars-cov-2 omicron ba.4/5 rbd in complex with human ace2 (local refinement) (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Omicron ba.4/5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (Complex from Homo sapiens)
Human PORCN in complex with Palmitoleoyl-CoA
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 7ura
Q-score: 0.557
Liu Y, Qi X, Donnelly L, Elghobashi-Meinhardt N, Long T, Zhou RW, Sun Y, Wang B, Li X
Nature (2022) 607 pp. 816-822 [ Pubmed: 35831507 DOI: doi:10.1038/s41586-022-04952-2 ]
- Zinc ion (65 Da, Ligand)
- Digitonin (1 kDa, Ligand)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (52 kDa, Protein from Homo sapiens)
- ~{s}-[2-[3-[[(2~{r})-4-[[[(2~{r},3~{r},4~{r},5~{r})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (~{z})-hexadec-9-enethioate (1 kDa, Ligand)
- 2c11 heavy chain (26 kDa, Protein from Mus musculus)
- Oleic acid (282 Da, Ligand)
- 16:1 coa-bound human porcn (Complex)
- Cholesterol (386 Da, Ligand)
- 2c11 light chain, 2c11 heavy chain (Complex from Mus musculus)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (e.c.2.3.1.250) (Complex from Homo sapiens)
- 2c11 light chain (25 kDa, Protein from Mus musculus)
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 7urc
Q-score: 0.532
Liu Y, Qi X, Donnelly L, Elghobashi-Meinhardt N, Long T, Zhou RW, Sun Y, Wang B, Li X
Nature (2022) 607 pp. 816-822 [ Pubmed: 35831507 DOI: doi:10.1038/s41586-022-04952-2 ]
- Zinc ion (65 Da, Ligand)
- Digitonin (1 kDa, Ligand)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (52 kDa, Protein from Homo sapiens)
- 2c11 heavy chain (26 kDa, Protein from Mus musculus)
- Lgk974-bound human porcn (Complex)
- 2-[(2p)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-n-[(5p)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide (396 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- 2c11 light chain, 2c11 heavy chain (Complex from Mus musculus)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (e.c.2.3.1.250) (Complex from Homo sapiens)
- 2c11 light chain (25 kDa, Protein from Mus musculus)
Resolution: 2.92 Å
EM Method: Single-particle
Fitted PDBs: 7urd
Q-score: 0.569
Liu Y, Qi X, Donnelly L, Elghobashi-Meinhardt N, Long T, Zhou RW, Sun Y, Wang B, Li X
Nature (2022) 607 pp. 816-822 [ Pubmed: 35831507 DOI: doi:10.1038/s41586-022-04952-2 ]
- Zinc ion (65 Da, Ligand)
- Isoform 2 of protein wnt-3a peptide (Complex)
- Digitonin (1 kDa, Ligand)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (52 kDa, Protein from Homo sapiens)
- 2c11 heavy chain (26 kDa, Protein from Mus musculus)
- Lgk974 and wnt3a peptide-bound human porcn (Complex)
- 2-[(2p)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-n-[(5p)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide (396 Da, Ligand)
- Oleic acid (282 Da, Ligand)
- Isoform 2 of protein wnt-3a peptide (2 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- 2c11 light chain, 2c11 heavy chain (Complex from Mus musculus)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (e.c.2.3.1.250) (Complex from Homo sapiens)
- 2c11 light chain (25 kDa, Protein from Mus musculus)
Human PORCN in complex with palmitoleoylated WNT3A peptide
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 7ure
Q-score: 0.539
Liu Y, Qi X, Donnelly L, Elghobashi-Meinhardt N, Long T, Zhou RW, Sun Y, Wang B, Li X
Nature (2022) 607 pp. 816-822 [ Pubmed: 35831507 DOI: doi:10.1038/s41586-022-04952-2 ]
- Zinc ion (65 Da, Ligand)
- Palmitoleic acid (254 Da, Ligand)
- Digitonin (1 kDa, Ligand)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (52 kDa, Protein from Homo sapiens)
- 2c11 heavy chain (26 kDa, Protein from Mus musculus)
- Protein wnt-3a (2 kDa, Protein from Homo sapiens)
- Isoform 2 of protein wnt-3a (Complex)
- Product-bound human porcn (Complex)
- 2c11 light chain, 2c11 heavy chain (Complex from Mus musculus)
- Isoform 2 of protein-serine o-palmitoleoyltransferase porcupine (e.c.2.3.1.250) (Complex from Homo sapiens)
- 2c11 light chain (25 kDa, Protein from Mus musculus)
SARS-CoV-2 S trimer with four-antibody cocktail complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7e5s
Q-score: 0.187
Sun Y, Wang L, Feng R, Wang N, Wang Y, Zhu D, Xing X, Yang P, Zhang Y, Li W, Wang X
Cell Res (2021) 31 pp. 597-600 [ Pubmed: 33782529 DOI: doi:10.1038/s41422-021-00497-7 ]
- P17 heavy chain (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Hb27 heavy chain (23 kDa, Protein from Homo sapiens)
- Four-antibody cocktail (Complex)
- P17 light chain (11 kDa, Protein from Homo sapiens)
- H014 heavy chain (23 kDa, Protein from Homo sapiens)
- Fc05 heavy chain (13 kDa, Protein from Homo sapiens)
- Fc05 light chain (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 s trimer (Complex from Homo sapiens)
- H014 light chain (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 s trimer with four-antibody cocktail complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- Hb27 light chain (12 kDa, Protein from Homo sapiens)