Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 7zlg
Q-score: 0.454
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in complex with acceptor peptide and bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Water (18 Da, Ligand)
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7zlj
Q-score: 0.411
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP
Nat Chem Biol (2023) 19 pp. 575-584 [ Pubmed: 36604564 DOI: doi:10.1038/s41589-022-01219-9 ]
- C-mannosyltransferase dpy-19 (80 kDa, Protein from Caenorhabditis elegans)
- Cmt2-fab heavy chain (25 kDa, Protein from synthetic construct)
- Anti-fab nanobody (13 kDa, Protein from synthetic construct)
- Cmt2-fab light chain (23 kDa, Protein from synthetic construct)
- [(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{s},6~{e},10~{z},14~{e})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid (600 Da, Ligand)
- Synthetic octapeptide wehi 1886493 (821 Da, Protein from synthetic construct)
- C-mannosyltransferase cedpy19, in ternary complex with dol25-p-c-man and acceptor peptide, bound to cmt2-fab and anti-fab nanobody (Complex from Caenorhabditis elegans)
- Water (18 Da, Ligand)
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 [ DOI: doi:10.1038/s41467-022-35067-x Pubmed: 36435935 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (31 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycotransferase (81 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)
- 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate (414 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1 (49 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (54 kDa, Protein from Saccharomyces cerevisiae)
- Peptide (682 Da, Protein from Saccharomyces cerevisiae)
- 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (758 Da, Ligand)
- Ost4 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost5 (9 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Manganese (ii) ion (54 Da, Ligand)
- Yeast ost complex with lipid-linked oligosaccharide and non-acceptor peptide bound (284 kDa, Complex from Saccharomyces cerevisiae)
- Ost3 isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
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 [ DOI: doi:10.1038/s41467-022-35067-x Pubmed: 36435935 ]
- (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)
- 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate (414 Da, Ligand)
- Phosphatidylethanolamine (734 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1 (49 kDa, Protein from Saccharomyces cerevisiae)
- Peptide (696 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)
- Yeast ost complex with acceptor peptide bound (284 kDa, Complex from Saccharomyces cerevisiae)
- Ost4 isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost5 (9 kDa, Protein from Saccharomyces cerevisiae)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ost2 (14 kDa, Protein from Saccharomyces cerevisiae)
- Manganese (ii) ion (54 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3 (81 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Ost3 isoform 1 (39 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6p25
Q-score: 0.47
Bai L, Kovach A, You Q, Kenny A, Li H
Nat Struct Mol Biol (2019) 26 pp. 704-711 [ Pubmed: 31285605 DOI: doi:10.1038/s41594-019-0262-6 ]
- Protein o-mannosyl transferase complex (Complex from Saccharomyces cerevisiae W303)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dolichyl-phosphate-mannose--protein mannosyltransferase 1 (92 kDa, Protein from Saccharomyces cerevisiae W303)
- 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (758 Da, Ligand)
- Dolichyl-phosphate-mannose--protein mannosyltransferase 2 (86 kDa, Protein from Saccharomyces cerevisiae W303)
- (3r)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate (644 Da, Ligand)
- Acceptor peptide (478 Da, Protein from Saccharomyces cerevisiae W303)