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.)
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 7wld
Q-score: 0.615
Xu Y, Jia G, Li T, Zhou Z, Luo Y, Chao Y, Bao J, Su Z, Qu Q, Li D
Nat Commun (2022) 13 pp. 2617-2617 [ Pubmed: 35551457 DOI: doi:10.1038/s41467-022-30250-6 ]
- [(2r)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate (720 Da, Ligand)
- Gpi transamidase component pig-t (94 kDa, Protein from Homo sapiens)
- Phosphatidylinositol glycan anchor biosynthesis class u protein (80 kDa, Protein from Homo sapiens)
- Gpi transamidase complex (Complex from Homo sapiens)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 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)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- O-[(r)-{[(2r)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-l-serine (792 Da, Ligand)
- Gpi transamidase component pig-s (90 kDa, Protein from Homo sapiens)
- Glycosylphosphatidylinositol anchor attachment 1 protein (96 kDa, Protein from Homo sapiens)
- Digitonin (1 kDa, Ligand)
- Gpi-anchor transamidase (73 kDa, Protein from Homo sapiens)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- 2-amino-2-deoxy-alpha-d-glucopyranose (179 Da, Ligand)
- [(2~{r})-1-hexadecanoyloxy-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{z},11~{z})-octadeca-9,11-dienoate (1 kDa, Ligand)
- (4s,7r)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-n,n,n-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium (763 Da, Ligand)
CryoEM structure of SGLT1 at 3.4 A resolution
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7sl8
Q-score: 0.467
Han L, Qu Q, Aydin D, Panova O, Robertson MJ, Xu Y, Dror RO, Skiniotis G, Feng L
Nature (2022) 601 pp. 274-279 [ Pubmed: 34880492 DOI: doi:10.1038/s41586-021-04211-w ]
- Nanobody nb1 (14 kDa, Protein from synthetic construct)
- Sodium/glucose cotransporter 1 (74 kDa, Protein from Homo sapiens)
- Cholesterol (386 Da, Ligand)
- Nanobody-sglt complex (Complex from Homo sapiens)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7sl9
Q-score: 0.463
Han L, Qu Q, Aydin D, Panova O, Robertson MJ, Xu Y, Dror RO, Skiniotis G, Feng L
Nature (2022) 601 pp. 274-279 [ Pubmed: 34880492 DOI: doi:10.1038/s41586-021-04211-w ]
- Butanoic acid (88 Da, Ligand)
- Sodium-coupled monocarboxylate transporter 1 (67 kDa, Protein from Homo sapiens)
- Smct1 and nanobody complex (Complex from Homo sapiens)
- Nanobody nb2 (14 kDa, Protein from synthetic construct)
CryoEM structure of SGLT1 at 3.15 angstrom resolution
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7sla
Q-score: 0.505
Han L, Qu Q, Aydin D, Panova O, Robertson MJ, Xu Y, Dror RO, Skiniotis G, Feng L
Nature (2022) 601 pp. 274-279 [ DOI: doi:10.1038/s41586-021-04211-w Pubmed: 34880492 ]
- Nanobody nb1 (14 kDa, Protein from synthetic construct)
- Cholesterol hemisuccinate (486 Da, Ligand)
- Sodium/glucose cotransporter 1 (74 kDa, Protein from Homo sapiens)
- Sglt1 and nanobody complex (Complex from Homo sapiens)