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 ]
- (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 2 (69 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- (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)
- Oligosaccharyltransferase complex ost-a with bound ngi-1 inhibitor (Complex from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 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)
- Manganese (ii) ion (54 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- 5-(dimethylsulfamoyl)-~{n}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide (394 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
Outer kinetochore Dam1 protomer dimer Ndc80-Nuf2 coiled-coil complex
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 8q84
Q-score: 0.294
Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D
Science (2023) 382 pp. 1184-1190 [ Pubmed: 38060647 DOI: doi:10.1126/science.adj8736 ]
- Dash complex subunit dam1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit duo1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Outer kinetochore dam1 protomer dimer with staple and ndc80-nuf2 coiled-coils (673 GDa, Complex from Saccharomyces cerevisiae)
- Kinetochore protein nuf2 (53 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit spc19 (18 kDa, Protein from Saccharomyces cerevisiae)
- Kinetochore protein ndc80 (80 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit spc34 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit hsk3 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad3 (10 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad2 (15 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit ask1 (32 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad1 (10 kDa, Protein from Saccharomyces cerevisiae)
Outer kinetochore Dam1 protomer monomer Ndc80-Nuf2 coiled-coil complex
Resolution: 3.97 Å
EM Method: Single-particle
Fitted PDBs: 8q85
Q-score: 0.277
Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D
Science (2023) 382 pp. 1184-1190 [ Pubmed: 38060647 DOI: doi:10.1126/science.adj8736 ]
- Dash complex subunit dam1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit duo1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Kinetochore protein nuf2 (53 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit spc19 (18 kDa, Protein from Saccharomyces cerevisiae)
- Kinetochore protein ndc80 (80 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit spc34 (34 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit hsk3 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad3 (10 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad2 (15 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit dad4 (8 kDa, Protein from Saccharomyces cerevisiae)
- Dash complex subunit ask1 (32 kDa, Protein from Saccharomyces cerevisiae)
- Outer kinetochore dam1 protomer monomer with staple and ndc80-nuf2 coiled-coils (673 GDa, Complex from Saccharomyces cerevisiae)
- Dash complex subunit dad1 (10 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Translocon-associated protein subunit gamma (21 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit alpha isoform 1 (52 kDa, Protein from Homo sapiens)
- Signal peptide mix (1 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Sec61-trap-osta translocon complex (Cellular component from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit alpha (32 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit beta (20 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit gamma (7 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Protein transport protein sec61 subunit beta (9 kDa, Protein from Homo sapiens)
- Translocon-associated protein subunit delta (19 kDa, Protein from Homo sapiens)
Negative stain EM 3D Reconstruction of the Dam1cBim1p complex.
Dudziak A, Engelhard L, Bourque C, Klink BU, Rombaut P, Kornakov N, Janen K, Herzog F, Gatsogiannis C, Westermann S
EMBO J (2021) 40 pp. e108004-e108004 [ Pubmed: 34313341 DOI: doi:10.15252/embj.2021108004 ]
- Dam1pbim1p complex (Complex from Saccharomyces cerevisiae)
- Spc19 protein of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad1p of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad2p of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad4p of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad3p of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Bim1p of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dam1 protein of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Hsk3p of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Duo1 protein of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Ask1 protein of the dam1c from s. cerevisiae (Protein from Saccharomyces cerevisiae)
Negative stain EM 3D reconstruction of the Dam1 / DASH complex.
Dudziak A, Engelhard L, Bourque C, Klink BU, Rombaut P, Kornakov N, Janen K, Herzog F, Gatsogiannis C, Westermann S
EMBO J (2021) 40 pp. e108004-e108004 [ Pubmed: 34313341 DOI: doi:10.15252/embj.2021108004 ]
- A dimer of the dam1 / dash complex. (3 MDa, Complex from Saccharomyces cerevisiae)
- Hsk3p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Spc34p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Duo1p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad1p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Spc19p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad2p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad3p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dad4p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Ask1p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
- Dam1p of the dam1c of s. cerevisiae (Protein from Saccharomyces cerevisiae)
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 ]
- (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 2 (69 kDa, Protein from Homo sapiens)
- Human oligosaccharyltransferase complex (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)
- Human oligosaccharyltransferase complex ost-a (Complex)
- Oligosaccharyltransferase complex subunit ostc (16 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 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)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit stt3a (80 kDa, Protein from Homo sapiens)
- Oligosaccharyltransferase complex subunit ostc (Complex from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 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 ]
- (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)
- Human oligosaccharyltransferase complex ost-b (Complex)
- Malectin (32 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (69 kDa, Protein from Homo sapiens)
- Human oligosaccharyltransferase complex (Complex from Homo sapiens)
- (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 stt3b (93 kDa, Protein from Homo sapiens)
- Transmembrane protein 258 (9 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (68 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit (50 kDa, Protein from Homo sapiens)
- Peptide (588 Da, 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)
- Magnesium transporter protein 1 (Complex from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 (4 kDa, Protein from Homo sapiens)
- Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad1 (12 kDa, Protein from Homo sapiens)
- Magnesium transporter protein 1 (38 kDa, Protein from Homo sapiens)
Science (2018) 360 pp. 552-558 [ DOI: doi:10.1126/science.aar6436 Pubmed: 29724956 ]
- Dad1 (Protein from Chaetomium thermophilum)
- Dad2 (Protein from Chaetomium thermophilum)
- Duo1 (Protein from Chaetomium thermophilum)
- Dad3 (Protein from Chaetomium thermophilum)
- Dad4 (Protein from Chaetomium thermophilum)
- Hsk3 (Protein from Chaetomium thermophilum)
- Dam1 (Protein from Chaetomium thermophilum)
- Dash/dam1 complex (115 kDa, Complex from Chaetomium thermophilum)
- Spc19 (Protein from Chaetomium thermophilum)
- Ask1 (Protein from Chaetomium thermophilum)
- Spc34 (Protein from Chaetomium thermophilum)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6cfz
Q-score: 0.208
Science (2018) 360 pp. 552-558 [ DOI: doi:10.1126/science.aar6436 Pubmed: 29724956 ]
- Spc34 (27 kDa, Protein from Chaetomium thermophilum)
- Ask1 (8 kDa, Protein from Chaetomium thermophilum)
- Spc19 (17 kDa, Protein from Chaetomium thermophilum)
- Dad1,dad1 (10 kDa, Protein from Chaetomium thermophilum)
- Dad4 (8 kDa, Protein from Chaetomium thermophilum)
- Dash/dam1 complex (115 kDa, Complex from Chaetomium thermophilum)
- Dad2 (10 kDa, Protein from Chaetomium thermophilum)
- Hsk3 (6 kDa, Protein from Chaetomium thermophilum)
- Dam1 (6 kDa, Protein from Chaetomium thermophilum)
- Duo1 (12 kDa, Protein from Chaetomium thermophilum)
- Dad3 (7 kDa, Protein from Chaetomium thermophilum)