+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16467 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the yeast SPT-Orm1-Monomer complex | |||||||||
Map data | yeast-SPOTS-Orm1-Monomer | |||||||||
Sample |
| |||||||||
Keywords | Serine-Palmitoyl-Transferase / SPT / Orm-Protein / TRANSFERASE | |||||||||
Function / homology | Function and homology information positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / negative regulation of sphingolipid biosynthetic process / serine C-palmitoyltransferase complex / SPOTS complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingolipid biosynthetic process / sphingosine biosynthetic process ...positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / negative regulation of sphingolipid biosynthetic process / serine C-palmitoyltransferase complex / SPOTS complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / sphingolipid biosynthetic process / sphingosine biosynthetic process / ceramide biosynthetic process / ceramide metabolic process / enzyme activator activity / response to unfolded protein / Neutrophil degranulation / pyridoxal phosphate binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Schaefer J / Koerner C / Parey K / Januliene D / Moeller A / Froehlich F | |||||||||
Funding support | Germany, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Structure of the ceramide-bound SPOTS complex. Authors: Jan-Hannes Schäfer / Carolin Körner / Bianca M Esch / Sergej Limar / Kristian Parey / Stefan Walter / Dovile Januliene / Arne Moeller / Florian Fröhlich / Abstract: Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. ...Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16467.map.gz | 290.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16467-v30.xml emd-16467.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16467_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_16467.png | 53.1 KB | ||
Filedesc metadata | emd-16467.cif.gz | 7 KB | ||
Others | emd_16467_half_map_1.map.gz emd_16467_half_map_2.map.gz | 285.7 MB 285.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16467 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16467 | HTTPS FTP |
-Related structure data
Related structure data | 8c80MC 8c81C 8c82C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_16467.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | yeast-SPOTS-Orm1-Monomer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.924 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: halfmap-A yeast-SPOTS-Orm1-Monomer
File | emd_16467_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | halfmap-A yeast-SPOTS-Orm1-Monomer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: halfmap-B yeast-SPOTS-Orm1-Monomer
File | emd_16467_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | halfmap-B yeast-SPOTS-Orm1-Monomer | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3
Entire | Name: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3 |
---|---|
Components |
|
-Supramolecule #1: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3
Supramolecule | Name: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 160 KDa |
-Macromolecule #1: Protein ORM1
Macromolecule | Name: Protein ORM1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 25.221674 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MTELDYQGTA EAASTSYSRN QTDLKPFPSA GSASSSIKTT EPVKDHRRRR AAAIISHVEP ETFEDENDQQ LLPNMNATWV DQRGAWIIH VVIIILLKLF YNLFPGVTTE WSWTLTNMTY VIGSYVMFHL IKGTPFDFNG GAYDNLTMWE QIDDETLYTP S RKFLISVP ...String: MTELDYQGTA EAASTSYSRN QTDLKPFPSA GSASSSIKTT EPVKDHRRRR AAAIISHVEP ETFEDENDQQ LLPNMNATWV DQRGAWIIH VVIIILLKLF YNLFPGVTTE WSWTLTNMTY VIGSYVMFHL IKGTPFDFNG GAYDNLTMWE QIDDETLYTP S RKFLISVP IALFLVSTHY AHYDLKLFSW NCFLTTFGAV VPKLPVTHRL RISIPGITGR AQIS UniProtKB: Protein ORM1 |
-Macromolecule #2: Serine palmitoyltransferase 1
Macromolecule | Name: Serine palmitoyltransferase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 64.98552 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MAHIPEVLPD YKDHDGDYKD HDIDYKDDDD KKSIPIPAFI VTTSSYLWYY FNLVLTQIPG GQFIVSYIKK SHHDDPYRTT VEIGLILYG IIYYLSKPQQ KKSLQAQKPN LSPQEIDALI EDWEPEPLVD PSATDEQSWR VAKTPVTMEM PIQNHITITR N NLQEKYTN ...String: MAHIPEVLPD YKDHDGDYKD HDIDYKDDDD KKSIPIPAFI VTTSSYLWYY FNLVLTQIPG GQFIVSYIKK SHHDDPYRTT VEIGLILYG IIYYLSKPQQ KKSLQAQKPN LSPQEIDALI EDWEPEPLVD PSATDEQSWR VAKTPVTMEM PIQNHITITR N NLQEKYTN VFNLASNNFL QLSATEPVKE VVKTTIKNYG VGACGPAGFY GNQDVHYTLE YDLAQFFGTQ GSVLYGQDFC AA PSVLPAF TKRGDVIVAD DQVSLPVQNA LQLSRSTVYY FNHNDMNSLE CLLNELTEQE KLEKLPAIPR KFIVTEGIFH NSG DLAPLP ELTKLKNKYK FRLFVDETFS IGVLGATGRG LSEHFNMDRA TAIDITVGSM ATALGSTGGF VLGDSVMCLH QRIG SNAYC FSACLPAYTV TSVSKVLKLM DSNNDAVQTL QKLSKSLHDS FASDDSLRSY VIVTSSPVSA VLHLQLTPAY RSRKF GYTC EQLFETMSAL QKKSQTNKFI EPYEEEEKFL QSIVDHALIN YNVLITRNTI VLKQETLPIV PSLKICCNAA MSPEEL KNA CESVKQSILA CCQESNK UniProtKB: Serine palmitoyltransferase 1 |
-Macromolecule #3: Serine palmitoyltransferase 2
Macromolecule | Name: Serine palmitoyltransferase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 63.189707 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNK HLDLLEHDGL APWFSNFESF YVRRIKMRID DCFSRPTTGV PGRFIRCIDR ISHNINEYFT YSGAVYPCMN L SSYNYLGF ...String: MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNK HLDLLEHDGL APWFSNFESF YVRRIKMRID DCFSRPTTGV PGRFIRCIDR ISHNINEYFT YSGAVYPCMN L SSYNYLGF AQSKGQCTDA ALESVDKYSI QSGGPRAQIG TTDLHIKAEK LVARFIGKED ALVFSMGYGT NANLFNAFLD KK CLVISDE LNHTSIRTGV RLSGAAVRTF KHGDMVGLEK LIREQIVLGQ PKTNRPWKKI LICAEGLFSM EGTLCNLPKL VEL KKKYKC YLFIDEAHSI GAMGPTGRGV CEIFGVDPKD VDILMGTFTK SFGAAGGYIA ADQWIIDRLR LDLTTVSYSE SMPA PVLAQ TISSLQTISG EICPGQGTER LQRIAFNSRY LRLALQRLGF IVYGVADSPV IPLLLYCPSK MPAFSRMMLQ RRIAV VVVA YPATPLIESR VRFCMSASLT KEDIDYLLRH VSEVGDKLNL KSNSGKSSYD GKRQRWDIEE VIRRTPEDCK DDKYFV N UniProtKB: Serine palmitoyltransferase 2 |
-Macromolecule #4: Serine palmitoyltransferase-regulating protein TSC3
Macromolecule | Name: Serine palmitoyltransferase-regulating protein TSC3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 9.590233 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MTQHKSSMVY IPTTKEAKRR NGKSEGILNT IEEVVEKLYW TYYIHLPFYL MASFDSFFLH VFFLTIFSLS FFGILKYCFL UniProtKB: Serine palmitoyltransferase-regulating protein TSC3 |
-Macromolecule #5: ERGOSTEROL
Macromolecule | Name: ERGOSTEROL / type: ligand / ID: 5 / Number of copies: 3 / Formula: ERG |
---|---|
Molecular weight | Theoretical: 396.648 Da |
Chemical component information | ChemComp-ERG: |
-Macromolecule #6: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
Macromolecule | Name: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide type: ligand / ID: 6 / Number of copies: 1 / Formula: Z8A |
---|---|
Molecular weight | Theoretical: 696.182 Da |
Chemical component information | ChemComp-Z8A: |
-Macromolecule #7: PYRIDOXAL-5'-PHOSPHATE
Macromolecule | Name: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: PLP |
---|---|
Molecular weight | Theoretical: 247.142 Da |
Chemical component information | ChemComp-PLP: |
-Macromolecule #8: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...
Macromolecule | Name: 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 type: ligand / ID: 8 / Number of copies: 1 / Formula: Q7G |
---|---|
Molecular weight | Theoretical: 1.165315 KDa |
Chemical component information | ChemComp-Q7G: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10.0 mg/mL |
---|---|
Buffer | pH: 6.8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 13604 / Average electron dose: 50.0 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 79 |
---|---|
Output model | PDB-8c80: |