+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33866 | |||||||||
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Title | Cryo-EM structure of SPT-ORMDL3 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ceramide / TRANSFERASE-inhibitor complex / TRANSFERASE-INHIBITOR COMPLEX complex | |||||||||
Function / homology | Function and homology information sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / sphingosine biosynthetic process ...sphinganine biosynthetic process / regulation of fat cell apoptotic process / negative regulation of ceramide biosynthetic process / sphingomyelin biosynthetic process / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / ceramide metabolic process / sphingosine biosynthetic process / regulation of smooth muscle contraction / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingolipid metabolic process / ceramide biosynthetic process / negative regulation of B cell apoptotic process / motor behavior / positive regulation of lipophagy / adipose tissue development / specific granule membrane / positive regulation of autophagy / myelination / secretory granule membrane / positive regulation of protein localization to nucleus / protein localization / pyridoxal phosphate binding / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Xie T / Liu P / Gong X | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Authors: Tian Xie / Peng Liu / Xinyue Wu / Feitong Dong / Zike Zhang / Jian Yue / Usha Mahawar / Faheem Farooq / Hisham Vohra / Qi Fang / Wenchen Liu / Binks W Wattenberg / Xin Gong / Abstract: The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This ...The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33866.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-33866-v30.xml emd-33866.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_33866.png | 42.3 KB | ||
Filedesc metadata | emd-33866.cif.gz | 6.3 KB | ||
Others | emd_33866_half_map_1.map.gz emd_33866_half_map_2.map.gz | 49.4 MB 49.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33866 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33866 | HTTPS FTP |
-Validation report
Summary document | emd_33866_validation.pdf.gz | 832.9 KB | Display | EMDB validaton report |
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Full document | emd_33866_full_validation.pdf.gz | 832.5 KB | Display | |
Data in XML | emd_33866_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_33866_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33866 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33866 | HTTPS FTP |
-Related structure data
Related structure data | 7yiyMC 7yiuC 7yj1C 7yj2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33866.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33866_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33866_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPT-ORMDL3 complex
Entire | Name: SPT-ORMDL3 complex |
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Components |
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-Supramolecule #1: SPT-ORMDL3 complex
Supramolecule | Name: SPT-ORMDL3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine palmitoyltransferase 2
Macromolecule | Name: Serine palmitoyltransferase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.00416 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ NGGLYKRPFN EAFEETPMLV AVLTYVGYGV LTLFGYLRD FLRYWRIEKC HHATEREEQK DFVSLYQDFE NFYTRNLYMR IRDNWNRPIC SVPGARVDIM ERQSHDYNWS F KYTGNIIK ...String: MRPEPGGCCC RRTVRANGCV ANGEVRNGYV RSSAAAAAAA AAGQIHHVTQ NGGLYKRPFN EAFEETPMLV AVLTYVGYGV LTLFGYLRD FLRYWRIEKC HHATEREEQK DFVSLYQDFE NFYTRNLYMR IRDNWNRPIC SVPGARVDIM ERQSHDYNWS F KYTGNIIK GVINMGSYNY LGFARNTGSC QEAAAKVLEE YGAGVCSTRQ EIGNLDKHEE LEELVARFLG VEAAMAYGMG FA TNSMNIP ALVGKGCLIL SDELNHASLV LGARLSGATI RIFKHNNMQS LEKLLKDAIV YGQPRTRRPW KKILILVEGI YSM EGSIVR LPEVIALKKK YKAYLYLDEA HSIGALGPTG RGVVEYFGLD PEDVDVMMGT FTKSFGASGG YIGGKKELID YLRT HSHSA VYATSLSPPV VEQIITSMKC IMGQDGTSLG KECVQQLAEN TRYFRRRLKE MGFIIYGNED SPVVPLMLYM PAKIG AFGR EMLKRNIGVV VVGFPATPII ESRARFCLSA AHTKEILDTA LKEIDEVGDL LQLKYSRHRL VPLLDRPFDE TTYEET ED UniProtKB: Serine palmitoyltransferase 2 |
-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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5.898994 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MATATEQWVL VEMVQALYEA PAYHLILEGI LILWIIRLLF SKTYKLQERS UniProtKB: Serine palmitoyltransferase 1 |
-Macromolecule #3: ORM1-like protein 3
Macromolecule | Name: ORM1-like protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.512594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNVGTAHSEV NPNTRVMNSR GIWLSYVLAI GLLHIVLLSI PFVSVPVVWT LTNLIHNMGM YIFLHTVKGT PFETPDQGKA RLLTHWEQM DYGVQFTASR KFLTITPIVL YFLTSFYTKY DQIHFVLNTV SLMSVLIPKL PQLHGVRIFG INKY UniProtKB: ORM1-like protein 3 |
-Macromolecule #4: Serine palmitoyltransferase small subunit A
Macromolecule | Name: Serine palmitoyltransferase small subunit A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.742409 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADYKDDDDK SGPDEVDASG RMAGMALARA WKQMSWFYYQ YLLVTALYML EPWERTVFNS MLVSIVGMAL YTGYVFMPQH IMAILHYFE IVQ UniProtKB: Serine palmitoyltransferase small subunit A |
-Macromolecule #5: Serine palmitoyltransferase 1
Macromolecule | Name: Serine palmitoyltransferase 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.925828 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DLTVKEKEEL IEEWQPEPLV PPVPKDHPAL NYNIVSGPPS HKTVVNGKEC INFASFNFLG LLDNPRVKAA ALASLKKYGV GTCGPRGFY GTFDVHLDLE DRLAKFMKTE EAIIYSYGFA TIASAIPAYS KRGDIVFVDR AACFAIQKGL QASRSDIKLF K HNDMADLE ...String: DLTVKEKEEL IEEWQPEPLV PPVPKDHPAL NYNIVSGPPS HKTVVNGKEC INFASFNFLG LLDNPRVKAA ALASLKKYGV GTCGPRGFY GTFDVHLDLE DRLAKFMKTE EAIIYSYGFA TIASAIPAYS KRGDIVFVDR AACFAIQKGL QASRSDIKLF K HNDMADLE RLLKEQEIED QKNPRKARVT RRFIVVEGLY MNTGTICPLP ELVKLKYKYK ARIFLEESLS FGVLGEHGRG VT EHYGINI DDIDLISANM ENALASIGGF CCGRSFVIDH QRLSGQGYCF SASLPPLLAA AAIEALNIME ENPGIFAVLK EKC GQIHKA LQGISGLKVV GESLSPAFHL QLEESTGSRE QDVRLLQEIV DQCMNRSIAL TQARYLEKEE KCLPPPSIRV VVTV EQTEE ELERAASTIK EVAQAVLL UniProtKB: Serine palmitoyltransferase 1 |
-Macromolecule #6: PYRIDOXAL-5'-PHOSPHATE
Macromolecule | Name: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLP |
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Molecular weight | Theoretical: 247.142 Da |
Chemical component information | ChemComp-PLP: |
-Macromolecule #7: N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide
Macromolecule | Name: N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide type: ligand / ID: 7 / Number of copies: 1 / Formula: Z1T |
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Molecular weight | Theoretical: 650.113 Da |
Chemical component information | ChemComp-Z1T: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 358765 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |