Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8k9q
Q-score: 0.563
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Gpi inositol-deacylase,fused thermostable green fluorescent protein (163 kDa, Protein from synthetic construct)
- Gpi inositol-deacylase (163 kDa, Complex from Thermochaetoides thermophila)
- (2~{s})-2-azanyl-3-[[(2~{r})-3-hexadecanoyloxy-2-[(~{z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid (762 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8k9r
Q-score: 0.604
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- Cholesterol (386 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Complex of the gpi inositol-deacylase with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- [(2~{r})-1-octadecoxy-3-[oxidanyl-[(2~{r},3~{r},5~{s},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate (853 Da, Ligand)
Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8k9t
Q-score: 0.585
Hong J, Li T, Chao Y, Xu Y, Zhu Z, Zhou Z, Gu W, Qu Q, Li D
Nat Commun (2024) 15 pp. 8-8 [ DOI: doi:10.1038/s41467-023-44568-2 Pubmed: 38167496 ]
- Alpha-d-mannopyranose (180 Da, Ligand)
- [(2~{r})-1-octadecoxy-3-[oxidanyl-[(2~{r},3~{r},5~{s},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{z},8~{z},11~{z},14~{z})-icosa-5,8,11,14-tetraenoate (873 Da, Ligand)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- Complex of pgap1 with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- Palmitic acid (256 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8imx
Q-score: 0.567
Xu Y, Li T, Zhou Z, Hong J, Chao Y, Zhu Z, Zhang Y, Qu Q, Li D
Nat Commun (2023) 14 pp. 5520-5520 [ Pubmed: 37684232 DOI: doi:10.1038/s41467-023-41281-y ]
- Glycosylphosphatidylinositol anchor attachment 1 protein,gfp-like fluorescent chromoprotein cfp484 (96 kDa, Protein from Clavularia sp.)
- Ul16-binding protein 2,gfp-like fluorescent chromoprotein cfp484 (35 kDa, Protein from Homo sapiens)
- Gpi transamidase component pig-t,gfp-like fluorescent chromoprotein cfp484 (94 kDa, Protein from Clavularia sp.)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- Phosphatidylinositol glycan anchor biosynthesis class u protein,gfp-like fluorescent chromoprotein cfp484 (77 kDa, Protein from Clavularia sp.)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Gpi-anchor transamidase,gfp-like fluorescent chromoprotein cfp484 (73 kDa, Protein from Clavularia sp.)
- [(2r)-1-hexadecanoyloxy-3-[[3-[[(2r)-3-hexadecanoyloxy-2-[(z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (z)-octadec-9-enoate (1 kDa, Ligand)
- Complex of gpi-t with a chimeric gpi-anchored protein (469 MDa, Complex from Homo sapiens)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Digitonin (1 kDa, Ligand)
- Met-ser-ser peptide (323 Da, Protein from synthetic construct)
- [(2r)-1-[[(1s,2r,3r,4s,5s,6r)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Gpi transamidase component pig-s,gfp-like fluorescent chromoprotein cfp484 (90 kDa, Protein from Clavularia sp.)
Cryo-EM structure of GPI-T (inactive mutant) with GPI and proULBP2, a proprotein substrate
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8imy
Q-score: 0.536
Xu Y, Li T, Zhou Z, Hong J, Chao Y, Zhu Z, Zhang Y, Qu Q, Li D
Nat Commun (2023) 14 pp. 5520-5520 [ Pubmed: 37684232 DOI: doi:10.1038/s41467-023-41281-y ]
- Glycosylphosphatidylinositol anchor attachment 1 protein,gfp-like fluorescent chromoprotein cfp484 (96 kDa, Protein from Clavularia sp.)
- Gpi-anchor transamidase,gfp-like fluorescent chromoprotein cfp484 (73 kDa, Protein from Clavularia sp.)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- 2-azanylethyl [(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate (303 Da, Ligand)
- Phosphatidylinositol glycan anchor biosynthesis class u protein,gfp-like fluorescent chromoprotein cfp484 (80 kDa, Protein from Clavularia sp.)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- [(2r)-1-hexadecanoyloxy-3-[[3-[[(2r)-3-hexadecanoyloxy-2-[(z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (z)-octadec-9-enoate (1 kDa, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Ul16-binding protein 2 (28 kDa, Protein from Homo sapiens)
- Digitonin (1 kDa, Ligand)
- [(2r)-1-[[(1s,2r,3r,4s,5s,6r)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5z,8z,11z,14z)-icosa-5,8,11,14-tetraenoate (1 kDa, Ligand)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Gpi transamidase component pig-t,gfp-like fluorescent chromoprotein cfp484 (92 kDa, Protein from Clavularia sp.)
- Complex of gpi-t (inactive mutant) with gpi and proulbp2 (463 MDa, Complex from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Gpi transamidase component pig-s,gfp-like fluorescent chromoprotein cfp484 (90 kDa, Protein from Clavularia sp.)
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, state2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7vdh
Q-score: 0.53
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature (2021) 600 pp. 164-169 [ DOI: doi:10.1038/s41586-021-04077-y Pubmed: 34789875 ]
- Cholesterol (386 Da, Ligand)
- Mas-related g-protein coupled receptor member x2 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Cryo-em structure of pseudoallergen receptor mrgprx2 complex with c48/80, state2 (Complex from Homo sapiens)
- Scfv (30 kDa, Protein from Homo sapiens)
- 2-[4-methoxy-3-[[2-methoxy-3-[[2-methoxy-5-[2-(methylamino)ethyl]phenyl]methyl]-5-[2-(methylamino)ethyl]phenyl]methyl]phenyl]-~{n}-methyl-ethanamine (519 Da, Ligand)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with circular cortistatin-14
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 7vdl
Q-score: 0.5
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature (2021) 600 pp. 164-169 [ DOI: doi:10.1038/s41586-021-04077-y Pubmed: 34789875 ]
- Cholesterol (386 Da, Ligand)
- Mas-related g-protein coupled receptor member x2 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Scfv (30 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- The pseudoallergen receptor mrgprx2 complex with circular cortistatin-14 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
- Circular cortistatin-14 (1 kDa, Protein from Homo sapiens)
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7vdm
Q-score: 0.531
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature (2021) 600 pp. 164-169 [ DOI: doi:10.1038/s41586-021-04077-y Pubmed: 34789875 ]
- Mas-related g-protein coupled receptor member x2 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Peptide from protachykinin-1 (1 kDa, Protein from Homo sapiens)
- The pseudoallergen receptor mrgprx2 complex with substance p (Complex from Homo sapiens)
- Scfv (30 kDa, Protein from Homo sapiens)
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with PAMP-12. state1
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 7vuy
Q-score: 0.509
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature (2021) 600 pp. 164-169 [ DOI: doi:10.1038/s41586-021-04077-y Pubmed: 34789875 ]
- Mas-related g-protein coupled receptor member x2 (37 kDa, Protein from Homo sapiens)
- Scfv (30 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Cryo-em structure of pseudoallergen receptor mrgprx2 complex with pamp-12, state1 (Complex from Homo sapiens)
Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with PAMP-12, state2
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 7vuz
Q-score: 0.459
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature (2021) 600 pp. 164-169 [ DOI: doi:10.1038/s41586-021-04077-y Pubmed: 34789875 ]
- Mas-related g-protein coupled receptor member x2 (37 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (6 kDa, Protein from Homo sapiens)
- Cryo-em structure of pseudoallergen receptor mrgprx2 complex with pamp-12, state2 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Scfv (30 kDa, Protein from Homo sapiens)