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)
- (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)
- Gpi inositol-deacylase (163 kDa, Complex from Thermochaetoides thermophila)
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 ]
- Gpi inositol-deacylase,mcherry protein (161 kDa, Protein from Psychromonas sp. B3M02)
- 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)
- 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)
- Cholesterol (386 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)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- 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 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 ]
- Palmitic acid (256 Da, Ligand)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- Alpha-d-mannopyranose (180 Da, Ligand)
- 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)
- Complex of pgap1 with a chimera gpi-anchored protein (194 kDa, Complex from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
- Cholesterol (386 Da, Ligand)
- Green fluorescent protein,complement decay-accelerating factor (29 kDa, Protein from Homo sapiens)
- [(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)