+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33874 | |||||||||
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Title | Cryo-EM structure of the monomeric atSPT-ORM1 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ceramide / TRANSFERASE-INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information positive regulation of serine C-palmitoyltransferase activity / regulation of sphingolipid biosynthetic process / multidimensional cell growth / leaf senescence / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / : / photomorphogenesis / serine C-palmitoyltransferase activity / pollen development ...positive regulation of serine C-palmitoyltransferase activity / regulation of sphingolipid biosynthetic process / multidimensional cell growth / leaf senescence / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / : / photomorphogenesis / serine C-palmitoyltransferase activity / pollen development / serine C-palmitoyltransferase / ceramide metabolic process / regulation of programmed cell death / sphingosine biosynthetic process / embryo development ending in seed dormancy / sphingolipid biosynthetic process / ceramide biosynthetic process / vacuole / response to endoplasmic reticulum stress / pyridoxal phosphate binding / response to oxidative stress / defense response to bacterium / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Xie T / Liu P / Gong X | |||||||||
Funding support | 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Mechanism of sphingolipid homeostasis revealed by structural analysis of SPT-ORM1 complex. Authors: Peng Liu / Tian Xie / Xinyue Wu / Gongshe Han / Sita D Gupta / Zike Zhang / Jian Yue / Feitong Dong / Kenneth Gable / Somashekarappa Niranjanakumari / Wanyuan Li / Lin Wang / Wenchen Liu / ...Authors: Peng Liu / Tian Xie / Xinyue Wu / Gongshe Han / Sita D Gupta / Zike Zhang / Jian Yue / Feitong Dong / Kenneth Gable / Somashekarappa Niranjanakumari / Wanyuan Li / Lin Wang / Wenchen Liu / Ruifeng Yao / Edgar B Cahoon / Teresa M Dunn / Xin Gong / Abstract: The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosynthesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond ...The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosynthesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond to cellular sphingolipid levels. However, the molecular basis underlying ORM/ORMDL-dependent homeostatic regulation of SPT is not well understood. We determined the cryo-electron microscopy structure of SPT-ORM1 complex, composed of LCB1, LCB2a, SPTssa, and ORM1, in an inhibited state. A ceramide molecule is sandwiched between ORM1 and LCB2a in the cytosolic membrane leaflet. Ceramide binding is critical for the ORM1-dependent SPT repression, and dihydroceramides and phytoceramides differentially affect this repression. A hybrid β sheet, formed by the amino termini of ORM1 and LCB2a and induced by ceramide binding, stabilizes the amino terminus of ORM1 in an inhibitory conformation. Our findings provide mechanistic insights into sphingolipid homeostatic regulation via the binding of ceramide to the SPT-ORM/ORMDL complex that may have implications for plant-specific processes such as the hypersensitive response for microbial pathogen resistance. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33874.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-33874-v30.xml emd-33874.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_33874.png | 40.8 KB | ||
Filedesc metadata | emd-33874.cif.gz | 6.4 KB | ||
Others | emd_33874_half_map_1.map.gz emd_33874_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33874 | HTTPS FTP |
-Validation report
Summary document | emd_33874_validation.pdf.gz | 865.6 KB | Display | EMDB validaton report |
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Full document | emd_33874_full_validation.pdf.gz | 865.1 KB | Display | |
Data in XML | emd_33874_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_33874_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33874 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33874 | HTTPS FTP |
-Related structure data
Related structure data | 7yjmMC 7yjkC 7yjnC 7yjoC 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_33874.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_33874_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33874_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPT-ORM1 complex
Entire | Name: SPT-ORM1 complex |
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Components |
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-Supramolecule #1: SPT-ORM1 complex
Supramolecule | Name: SPT-ORM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: atLCB1
Macromolecule | Name: atLCB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 46.276117 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PLTEQEIDEL CDEWVPEPLI PPITEDMKHE PPVLESAAGP HTTVNGKDVV NFASANYLGL IGHEKLLESC TSALEKYGVG SCGPRGFYG TIDVHLDCET RISKFLGTPD SILYSYGLST MFSTIPCFCK KGDVIVADEG VHWGIQNGLQ LSRSTIVYFK H NDMESLRI ...String: PLTEQEIDEL CDEWVPEPLI PPITEDMKHE PPVLESAAGP HTTVNGKDVV NFASANYLGL IGHEKLLESC TSALEKYGVG SCGPRGFYG TIDVHLDCET RISKFLGTPD SILYSYGLST MFSTIPCFCK KGDVIVADEG VHWGIQNGLQ LSRSTIVYFK H NDMESLRI TLEKIMTKYK RSKNLRRYIV AEAVYQNSGQ IAPLDEIVKL KEKYRFRVIL DESNSFGVLG RSGRGLAEHH SV PIEKIDV VTAAMGHALA TEGGFCTGNA RIIDYQRLSS SGYVFSASLP PYLASAAITA IDVIDQNPDM LVKLKQNVAL LWK GLSDIK GMSLTSNRES PIVFLKLEKS SGSAKDDLLL LEKMADRALK EDSLLVVSSK RSFLDKCRLP VGIKLYVSAG HSES DLLKA SESLKRLASE LLLKS UniProtKB: Long chain base biosynthesis protein 1 |
-Macromolecule #2: Long chain base biosynthesis protein 2a
Macromolecule | Name: Long chain base biosynthesis protein 2a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 54.359457 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG HEDFYIRRLY HRIQDCFERP ISSAPDAWFD VVERYSNDN NKTLKRTTKT SRCLNLGSYN YLGFGSFDEY CTPRVIESLK KFSASTCSSR VDAGTTSVHA ELEECVTRFV G KPAAVVFG ...String: MITIPYLTAV STYFSYGLLF AFGQLRDFFR RFIDWWFTSN LQGYAPICLG HEDFYIRRLY HRIQDCFERP ISSAPDAWFD VVERYSNDN NKTLKRTTKT SRCLNLGSYN YLGFGSFDEY CTPRVIESLK KFSASTCSSR VDAGTTSVHA ELEECVTRFV G KPAAVVFG MGYATNSAII PVLIGKGGLI ISDSLNHSSI VNGARGSGAT IRVFQHNTPS HLERVLREQI AEGQPRTHRP WK KIIVVVE GIYSMEGEIC HLPEVVAICK KYKAYVYLDE AHSIGAIGKT GKGICELLGV DTADVDVMMG TFTKSFGSCG GYI AGSKEL IQYLKHQCPA HLYATSIPTP SAQQIISAIK VILGEDGSNR GAQKLARIRE NSNFFRAELQ KMGFEVLGDN DSPV MPIML YNPAKIPAFS RECLRQKVAV VVVGFPATPL LLARARICIS ASHSREDLIR ALKVISKVGD LSGIKYFPAE PKKIE QSKN DIKLD UniProtKB: Long chain base biosynthesis protein 2a |
-Macromolecule #3: ORMDL family protein
Macromolecule | Name: ORMDL family protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 18.220266 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MANLYVKAVP PPDMNRNTEW FMYPGVWTTY MLILFFGWLV VLSVSGCSPG MAWTVVNLAH FVVTYHSFHW MKGTPFADDQ GIYNGLTWW EQMDNGQQLT RNRKFLTLVP VVLYLIASHT TDYRHPWLFL NTLAVMVLVV AKFPNMHKVR IFGINGDK UniProtKB: ORMDL family protein |
-Macromolecule #4: atLCB1
Macromolecule | Name: atLCB1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 6.949384 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASNLVEMFN AALNWVTMIL ESPSARVVLF GVPIRGHFFV EGLLGVVIII LLTRKSYKPP KR UniProtKB: Long chain base biosynthesis protein 1 |
-Macromolecule #5: Transmembrane protein, putative (DUF3317)
Macromolecule | Name: Transmembrane protein, putative (DUF3317) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 9.442687 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADYKDDDDK SGPDEVDASG RMNWVQRKIY LYNVTFGLYM LDWWERYLFN SLVVVLMWFV LYNGTRYFSE LFQRHLT UniProtKB: Transmembrane protein, putative (DUF3317) |
-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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115440 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |