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 (163 kDa, Complex from Thermochaetoides thermophila)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Gpi inositol-deacylase,fused thermostable green fluorescent protein (163 kDa, Protein from synthetic construct)
- (2~{s})-2-azanyl-3-[[(2~{r})-3-hexadecanoyloxy-2-[(~{z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid (762 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 ]
- 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))
- Palmitic acid (256 Da, Ligand)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 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] octadecanoate (853 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)
- Cholesterol (386 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- Alpha-d-mannopyranose (180 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 ]
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- Palmitic acid (256 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-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Complex of pgap1 with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- 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)
- Cholesterol (386 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- Alpha-d-mannopyranose (180 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 [ DOI: doi:10.1038/s41467-023-41281-y Pubmed: 37684232 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Digitonin (1 kDa, Ligand)
- Gpi-anchor transamidase,gfp-like fluorescent chromoprotein cfp484 (73 kDa, Protein from Clavularia sp.)
- [(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)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Ul16-binding protein 2,gfp-like fluorescent chromoprotein cfp484 (35 kDa, Protein from Homo sapiens)
- Phosphatidylinositol glycan anchor biosynthesis class u protein,gfp-like fluorescent chromoprotein cfp484 (77 kDa, Protein from Clavularia sp.)
- 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.)
- Gpi transamidase component pig-t,gfp-like fluorescent chromoprotein cfp484 (94 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)
- Glycosylphosphatidylinositol anchor attachment 1 protein,gfp-like fluorescent chromoprotein cfp484 (96 kDa, Protein from Clavularia sp.)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- Met-ser-ser peptide (323 Da, Protein from synthetic construct)
- Calcium ion (40 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)
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 [ DOI: doi:10.1038/s41467-023-41281-y Pubmed: 37684232 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 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)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Complex of gpi-t (inactive mutant) with gpi and proulbp2 (463 MDa, Complex from Homo sapiens)
- Gpi transamidase component pig-t,gfp-like fluorescent chromoprotein cfp484 (92 kDa, Protein from Clavularia sp.)
- Ul16-binding protein 2 (28 kDa, Protein from Homo sapiens)
- Gpi-anchor transamidase,gfp-like fluorescent chromoprotein cfp484 (73 kDa, Protein from Clavularia sp.)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Phosphatidylinositol glycan anchor biosynthesis class u protein,gfp-like fluorescent chromoprotein cfp484 (80 kDa, Protein from Clavularia sp.)
- Gpi transamidase component pig-s,gfp-like fluorescent chromoprotein cfp484 (90 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)
- Glycosylphosphatidylinositol anchor attachment 1 protein,gfp-like fluorescent chromoprotein cfp484 (96 kDa, Protein from Clavularia sp.)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- 2-azanylethyl [(2r,3s,4s,5s,6s)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate (303 Da, Ligand)
- Calcium ion (40 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)