+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29860 | |||||||||||||||
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Title | Structure of inhibitor 16d-bound SPNS2 | |||||||||||||||
Map data | Structure of inhibitor 16d-bound SPNS2 | |||||||||||||||
Sample |
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Keywords | SPNS2 / Sphingosine-1-phosphate / major facilitator superfamily / transporter / IMMUNE SYSTEM | |||||||||||||||
Function / homology | Function and homology information regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / lipid transport / T cell homeostasis ...regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / lipid transport / T cell homeostasis / B cell homeostasis / transmembrane transporter activity / lymph node development / sensory perception of sound / bone development / endosome membrane / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Chen H / Li X | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Cell / Year: 2023 Title: Structural and functional insights into Spns2-mediated transport of sphingosine-1-phosphate. Authors: Hongwen Chen / Shahbaz Ahmed / Hongtu Zhao / Nadia Elghobashi-Meinhardt / Yaxin Dai / Jae Hun Kim / Jeffrey G McDonald / Xiaochun Li / Chia-Hsueh Lee / Abstract: Sphingosine-1-phosphate (S1P) is an important signaling sphingolipid that regulates the immune system, angiogenesis, auditory function, and epithelial and endothelial barrier integrity. Spinster ...Sphingosine-1-phosphate (S1P) is an important signaling sphingolipid that regulates the immune system, angiogenesis, auditory function, and epithelial and endothelial barrier integrity. Spinster homolog 2 (Spns2) is an S1P transporter that exports S1P to initiate lipid signaling cascades. Modulating Spns2 activity can be beneficial in treatments of cancer, inflammation, and immune diseases. However, the transport mechanism of Spns2 and its inhibition remain unclear. Here, we present six cryo-EM structures of human Spns2 in lipid nanodiscs, including two functionally relevant intermediate conformations that link the inward- and outward-facing states, to reveal the structural basis of the S1P transport cycle. Functional analyses suggest that Spns2 exports S1P via facilitated diffusion, a mechanism distinct from other MFS lipid transporters. Finally, we show that the Spns2 inhibitor 16d attenuates the transport activity by locking Spns2 in the inward-facing state. Our work sheds light on Spns2-mediated S1P transport and aids the development of advanced Spns2 inhibitors. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29860.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-29860-v30.xml emd-29860.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29860_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_29860.png | 47.1 KB | ||
Filedesc metadata | emd-29860.cif.gz | 5.8 KB | ||
Others | emd_29860_half_map_1.map.gz emd_29860_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29860 | HTTPS FTP |
-Validation report
Summary document | emd_29860_validation.pdf.gz | 898.5 KB | Display | EMDB validaton report |
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Full document | emd_29860_full_validation.pdf.gz | 898.1 KB | Display | |
Data in XML | emd_29860_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_29860_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29860 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29860 | HTTPS FTP |
-Related structure data
Related structure data | 8g92MC 8ex4C 8ex5C 8ex6C 8ex7C 8ex8C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29860.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Structure of inhibitor 16d-bound SPNS2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_29860_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_29860_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPNS2 in complex with inhibitor 16d
Entire | Name: SPNS2 in complex with inhibitor 16d |
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Components |
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-Supramolecule #1: SPNS2 in complex with inhibitor 16d
Supramolecule | Name: SPNS2 in complex with inhibitor 16d / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Sphingosine-1-phosphate transporter SPNS2
Macromolecule | Name: Sphingosine-1-phosphate transporter SPNS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.770148 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EKRKAEEEKR KAAAAILSLG NVLNYLDRYT VAGVLLDIQQ HFGVKDRGAG LLQSVFICSF MVAAPIFGYL GDRFNRKVIL SCGIFFWSA VTFSSSFIPQ QYFWLLVLSR GLVGIGEASY STIAPTIIGD LFTKNTRTLM LSVFYFAIPL GSGLGYITGS S VKQAAGDW ...String: EKRKAEEEKR KAAAAILSLG NVLNYLDRYT VAGVLLDIQQ HFGVKDRGAG LLQSVFICSF MVAAPIFGYL GDRFNRKVIL SCGIFFWSA VTFSSSFIPQ QYFWLLVLSR GLVGIGEASY STIAPTIIGD LFTKNTRTLM LSVFYFAIPL GSGLGYITGS S VKQAAGDW HWALRVSPVL GMITGTLILI LVPATKRGHA DQLGDQLKAR TSWLRDMKAL IRNRSYVFSS LATSAVSFAT GA LGMWIPL YLHRAQVVQK TAETCNSPPC GAKDSLIFGA ITCFTGFLGV VTGAGATRWC RLKTQRADPL VCAVGMLGSA IFI CLIFVA AKSSIVGAYI CIFVGETLLF SNWAITADIL MYVVIPTRRA TAVALQSFTS HLLGDAGSPY LIGFISDLIR QSTK DSPLW EFLSLGYALM LCPFVVVLGG MFFLATALFF VSDRARAEQQ VNQLAMPPAS VKV UniProtKB: Sphingosine-1-phosphate transporter SPNS2 |
-Macromolecule #2: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine
Macromolecule | Name: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine type: ligand / ID: 2 / Number of copies: 1 / Formula: YUX |
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Molecular weight | Theoretical: 343.506 Da |
Chemical component information | ChemComp-YUX: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |