Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1
Resolution: 3.61 Å
EM Method: Single-particle
Fitted PDBs: 8pn9
Q-score: 0.474
Lampson BL, Ramirez AS, Baro M, He L, Hegde M, Koduri V, Pfaff JL, Hanna RE, Kowal J, Shirole NH, He Y, Doench JG, Contessa JN, Locher KP, Kaelin Jr WG
Cell (2024) 187 pp. 2209-2223.e16 [ DOI: doi:10.1016/j.cell.2024.03.022 Pubmed: 38670073 ]
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Oligosaccharyltransferase complex ost-a with bound ngi-1 inhibitor (Complex from Homo sapiens)
- (4r,7r)-4-hydroxy-n,n,n-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium (636 Da, Ligand)
- 5-(dimethylsulfamoyl)-~{n}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide (394 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- (2~{s},3~{r},4~{r},5~{s},6~{s})-2-(hydroxymethyl)-6-[(1~{s},2~{r},3~{r},4~{r},5'~{s},6~{s},7~{r},8~{s},9~{r},12~{r},13~{r},15~{s},16~{s},18~{r})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol (610 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- (2e,6e,10e,14e,18e,22e,26e)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaenyl trihydrogen diphosphate (722 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8agc
Q-score: 0.548
Ramirez AS, de Capitani M, Pesciullesi G, Kowal J, Bloch JS, Irobalieva RN, Reymond JL, Aebi M, Locher KP
Nat Commun (2022) 13 pp. 7296-7296 [ Pubmed: 36435935 DOI: doi:10.1038/s41467-022-35067-x ]
- Dolichyl-diphosphooligosaccharide--protein glycotransferase (81 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ost complex with lipid-linked oligosaccharide and non-acceptor peptide bound (284 kDa, Complex from Saccharomyces cerevisiae)
- Peptide (682 Da, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (54 kDa, Protein from Saccharomyces cerevisiae)
- 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (758 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1 (49 kDa, Protein from Saccharomyces cerevisiae)
- Ost4 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- Ost3 isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (31 kDa, Protein from Saccharomyces cerevisiae)
- Manganese (ii) ion (54 Da, Ligand)
- 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate (414 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost5 (9 kDa, Protein from Saccharomyces cerevisiae)
- Phosphono [(3~{r},6~{e},10~{e})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate (452 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
Structure of yeast oligosaccharylransferase complex with acceptor peptide bound
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8age
Q-score: 0.571
Ramirez AS, de Capitani M, Pesciullesi G, Kowal J, Bloch JS, Irobalieva RN, Reymond JL, Aebi M, Locher KP
Nat Commun (2022) 13 pp. 7296-7296 [ Pubmed: 36435935 DOI: doi:10.1038/s41467-022-35067-x ]
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3 (81 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ost complex with acceptor peptide bound (284 kDa, Complex from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (54 kDa, Protein from Saccharomyces cerevisiae)
- 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (758 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1 (49 kDa, Protein from Saccharomyces cerevisiae)
- Ost4 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- Ost3 isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
- (2~{s},3~{r},4~{r},5~{s},6~{s})-2-(hydroxymethyl)-6-[(1~{s},2~{r},3~{r},4~{r},5'~{s},6~{s},7~{r},8~{s},9~{r},12~{r},13~{r},15~{s},16~{s},18~{r})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol (610 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (31 kDa, Protein from Saccharomyces cerevisiae)
- Manganese (ii) ion (54 Da, Ligand)
- 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate (414 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost5 (9 kDa, Protein from Saccharomyces cerevisiae)
- Peptide (696 Da, Protein from Saccharomyces cerevisiae)
- Phosphatidylethanolamine (734 Da, Ligand)
Subtomogram average of the human Sec61-TRAP-OSTA-translocon
Resolution: 7.6 Å
EM Method: Subtomogram averaging
Fitted PDBs: 8b6l
Q-score: 0.133
Gemmer M, Chaillet ML, van Loenhout J, Cuevas Arenas R, Vismpas D, Grollers-Mulderij M, Koh FA, Albanese P, Scheltema RA, Howes SC, Kotecha A, Fedry J, Forster F
Nature (2023) 614 pp. 160-167 [ DOI: doi:10.1038/s41586-022-05638-5 Pubmed: 36697828 ]
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit beta (20 kDa, Protein from Homo sapiens)
- Signal peptide mix (1 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit gamma (21 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit alpha (32 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit delta (19 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Sec61-trap-osta translocon complex (Cellular component from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
Cryo-EM structure of human oligosaccharyltransferase complex OST-A
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6s7o
Q-score: 0.485
Ramirez AS, Kowal J, Locher KP
Science (2019) 366 pp. 1372-1375 [ Pubmed: 31831667 DOI: doi:10.1126/science.aaz3505 ]
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Human oligosaccharyltransferase complex (Complex from Homo sapiens)
- (4r,7r)-4-hydroxy-n,n,n-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium (636 Da, Ligand)
- Human oligosaccharyltransferase complex ost-a (Complex)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (Complex from Homo sapiens)
- [(3~{r},6~{z},10~{z},14~{z},18~{z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate (508 Da, Ligand)
- (2~{s},3~{r},4~{r},5~{s},6~{s})-2-(hydroxymethyl)-6-[(1~{s},2~{r},3~{r},4~{r},5'~{s},6~{s},7~{r},8~{s},9~{r},12~{r},13~{r},15~{s},16~{s},18~{r})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol (610 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
Cryo-EM structure of human oligosaccharyltransferase complex OST-B
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6s7t
Q-score: 0.509
Ramirez AS, Kowal J, Locher KP
Science (2019) 366 pp. 1372-1375 [ Pubmed: 31831667 DOI: doi:10.1126/science.aaz3505 ]
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Human oligosaccharyltransferase complex ost-b (Complex)
- Human oligosaccharyltransferase complex (Complex from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Magnesium transporter protein 1 (38 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3b (93 kDa, Protein from Homo sapiens)
- Magnesium transporter protein 1 (Complex from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Peptide (588 Da, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- (2~{s},3~{r},4~{r},5~{s},6~{s})-2-(hydroxymethyl)-6-[(1~{s},2~{r},3~{r},4~{r},5'~{s},6~{s},7~{r},8~{s},9~{r},12~{r},13~{r},15~{s},16~{s},18~{r})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol (610 Da, Ligand)
- Malectin (32 kDa, Protein from Homo sapiens)
- (4r,7r)-4-hydroxy-n,n,n-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium (636 Da, Ligand)
- (2z,6z,10z,14z,18z,22z,26z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate (642 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)