Cryo-EM structure of the yeast SPT-Orm2-Dimer complex, local refinement of a monomer
Korner C, Schafer JH, Esch BM, Parey K, Walter S, Teis D, Januliene D, Schmidt O, Moeller A, Frohlich F
Cell Rep (2024) 43 pp. 114627-114627 [ Pubmed: 39167489 DOI: doi:10.1016/j.celrep.2024.114627 ]
- Complex of lcb1, lcb2, orm2 and tsc3 (160 kDa, Complex from Saccharomyces cerevisiae)
Cryo-EM structure of the yeast SPT-Orm2-Dimer complex
Korner C, Schafer JH, Esch BM, Parey K, Walter S, Teis D, Januliene D, Schmidt O, Moeller A, Frohlich F
Cell Rep (2024) 43 pp. 114627-114627 [ Pubmed: 39167489 DOI: doi:10.1016/j.celrep.2024.114627 ]
- Serine palmitoyltransferase 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase-regulating protein tsc3 (9 kDa, Protein from Saccharomyces cerevisiae)
- ~{n}-[(2~{s},3~{s},4~{r})-1,3,4-tris(oxidanyl)octadecan-2-yl]heptacosanamide (710 Da, Ligand)
- Orm2 isoform 1 (24 kDa, Protein from Saccharomyces cerevisiae)
- C2 symmetric complex of lcb1, lcb2, orm2 and tsc3 (320 kDa, Complex from Saccharomyces cerevisiae)
- Serine palmitoyltransferase 2 (63 kDa, Protein from Saccharomyces cerevisiae)
- Pyridoxal-5'-phosphate (247 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
Cryo-EM structure of the yeast SPT-Orm2-Monomer complex
Korner C, Schafer JH, Esch BM, Parey K, Walter S, Teis D, Januliene D, Schmidt O, Moeller A, Frohlich F
Cell Rep (2024) 43 pp. 114627-114627 [ Pubmed: 39167489 DOI: doi:10.1016/j.celrep.2024.114627 ]
- Serine palmitoyltransferase 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase-regulating protein tsc3 (9 kDa, Protein from Saccharomyces cerevisiae)
- ~{n}-[(2~{s},3~{s},4~{r})-1,3,4-tris(oxidanyl)octadecan-2-yl]heptacosanamide (710 Da, Ligand)
- Pyridoxal-5'-phosphate (247 Da, Ligand)
- Orm2 isoform 1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase 2 (63 kDa, Protein from Saccharomyces cerevisiae)
- C2 symmetric complex of lcb1, lcb2, orm2 and tsc3 (160 kDa, Complex from Saccharomyces cerevisiae)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
Cryo-EM structure of the yeast SPT-Orm1-Monomer complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8c80
Q-score: 0.463
Schafer JH, Korner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Frohlich F
Nat Commun (2023) 14 pp. 6196-6196 [ DOI: doi:10.1038/s41467-023-41747-z Pubmed: 37794019 ]
- Serine palmitoyltransferase 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase-regulating protein tsc3 (9 kDa, Protein from Saccharomyces cerevisiae)
- Pyridoxal-5'-phosphate (247 Da, Ligand)
- Protein orm1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Heterotetrameric complex of orm1 with lcb1, lcb2 and tsc3 (160 kDa, Complex from Saccharomyces cerevisiae)
- Serine palmitoyltransferase 2 (63 kDa, Protein from Saccharomyces cerevisiae)
- N-[(2s,3s,4r)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide (696 Da, Ligand)
- Ergosterol (396 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8c81
Q-score: 0.525
Schafer JH, Korner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Frohlich F
Nat Commun (2023) 14 pp. 6196-6196 [ DOI: doi:10.1038/s41467-023-41747-z Pubmed: 37794019 ]
- Serine palmitoyltransferase 1 (64 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase-regulating protein tsc3 (9 kDa, Protein from Saccharomyces cerevisiae)
- Pyridoxal-5'-phosphate (247 Da, Ligand)
- Heteropentameric complex of orm1 with lcb1, lcb2, tsc3 and sac1 (230 kDa, Complex from Saccharomyces cerevisiae)
- Protein orm1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase 2 (63 kDa, Protein from Saccharomyces cerevisiae)
- N-[(2s,3s,4r)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide (696 Da, Ligand)
- Ergosterol (396 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
- Phosphatidylinositol-3-phosphatase sac1 (71 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the yeast SPT-Orm1-Dimer complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8c82
Q-score: 0.488
Schafer JH, Korner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Frohlich F
Nat Commun (2023) 14 pp. 6196-6196 [ DOI: doi:10.1038/s41467-023-41747-z Pubmed: 37794019 ]
- Serine palmitoyltransferase 1 (62 kDa, Protein from Saccharomyces cerevisiae)
- Complex of orm1 with lcb1, lcb2 and tsc3 (325 kDa, Complex from Saccharomyces cerevisiae)
- Serine palmitoyltransferase-regulating protein tsc3 (9 kDa, Protein from Saccharomyces cerevisiae)
- Protein orm1 (25 kDa, Protein from Saccharomyces cerevisiae)
- Serine palmitoyltransferase 2 (63 kDa, Protein from Saccharomyces cerevisiae)
- N-[(2s,3s,4r)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide (696 Da, Ligand)
- Pyridoxal-5'-phosphate (247 Da, Ligand)
- 2-{[(4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-alpha-d-glucopyranoside (1 kDa, Ligand)
Cryo-EM structure of the yeast SPT-Orm1-Dimer complex, local refinement of a monomer
Schafer JH, Korner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Frohlich F
Nat Commun (2023) 14 pp. 6196-6196 [ DOI: doi:10.1038/s41467-023-41747-z Pubmed: 37794019 ]
Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7ph2
Q-score: 0.394
Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA
Sci Adv (2022) 8 pp. eabn6845-eabn6845 [ Pubmed: 36223470 DOI: doi:10.1126/sciadv.abn6845 ]
- (1~{r},4~{r},11~{s},14~{s},19~{z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione (524 Da, Ligand)
- Atp-dependent lipid a-core flippase (65 kDa, Protein from Escherichia coli K-12)
- E. coli msba in complex with nanobody nb_msba#1, labeled with gd-dota at cys60 (Complex from Escherichia coli)
- Gadolinium atom (157 Da, Ligand)
- Nb_msba#1 (12 kDa, Protein from Vicugna pacos)
- (2~{r},4~{r},5~{r},6~{r})-6-[(1~{r})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{s},5~{r},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-4-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[(1~{s})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{r},3~{s},4~{r},5~{r},6~{r})-4-[(3~{r})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{r})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{r},3~{s},4~{s},5~{s},6~{r})-3-oxidanyl-5-[[(3~{r})-3-oxidanylnonanoyl]amino]-4-[(3~{r})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic acid (2 kDa, Ligand)
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7ph3
Q-score: 0.555
Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA
Sci Adv (2022) 8 pp. eabn6845-eabn6845 [ Pubmed: 36223470 DOI: doi:10.1126/sciadv.abn6845 ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Atp-dependent lipid a-core flippase (65 kDa, Protein from Escherichia coli K-12)
- (1~{r},4~{r},11~{s},14~{s},19~{z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione (524 Da, Ligand)
- Water (18 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- E. coli msba in complex with nanobody nb_msba#1, labeled with gd-dota at cys60 (Complex from Escherichia coli)
- Gadolinium atom (157 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Nanobody nb_msba#1 (12 kDa, Protein from Vicugna pacos)
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7ph4
Q-score: 0.569
Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schafer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA
Sci Adv (2022) 8 pp. eabn6845-eabn6845 [ Pubmed: 36223470 DOI: doi:10.1126/sciadv.abn6845 ]
- Magnesium ion (24 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- (1~{r},4~{r},11~{s},14~{s},19~{z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione (524 Da, Ligand)
- Nanobody nb_msba#1 (12 kDa, Protein from Vicugna pacos)
- Water (18 Da, Ligand)
- Atp-dependent lipid a-core flippase (65 kDa, Protein from Escherichia coli (strain K12))
- Gadolinium atom (157 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Amp-pnp bound e. coli msba in complex with nanobody nb_msba#1, labeled with gd-dota at t68c (Complex)