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Yorodumi- EMDB-36284: Cryo-EM structure of human S1P transporter SPNS2 bound with S1P -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36284 | |||||||||
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Title | Cryo-EM structure of human S1P transporter SPNS2 bound with S1P | |||||||||
Map data | SPNS2 fusion full map | |||||||||
Sample |
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Keywords | Transpoter / LIPID TRANSPORT | |||||||||
Function / homology | Function and homology information regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / glycogen biosynthetic process ...regulation of eye pigmentation / regulation of humoral immune response / regulation of T cell migration / sphingolipid transporter activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / lymphocyte migration / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / sphingosine-1-phosphate receptor signaling pathway / glycogen biosynthetic process / lipid transport / T cell homeostasis / B cell homeostasis / transmembrane transporter activity / lymph node development / bone development / sensory perception of sound / endosome membrane / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Pang B / Yu LY / Ren RB | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Molecular basis of Spns2-facilitated sphingosine-1-phosphate transport. Authors: Bin Pang / Leiye Yu / Tong Li / Haizhan Jiao / Xiaomei Wu / Jinxin Wang / Ruiping He / Yurou Zhang / Juan Wang / Hongli Hu / Wei Dai / Li Chen / Ruobing Ren / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36284.map.gz | 85.7 MB | EMDB map data format | |
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Header (meta data) | emd-36284-v30.xml emd-36284.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_36284.png | 41.3 KB | ||
Filedesc metadata | emd-36284.cif.gz | 5.8 KB | ||
Others | emd_36284_half_map_1.map.gz emd_36284_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36284 | HTTPS FTP |
-Validation report
Summary document | emd_36284_validation.pdf.gz | 825.3 KB | Display | EMDB validaton report |
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Full document | emd_36284_full_validation.pdf.gz | 824.9 KB | Display | |
Data in XML | emd_36284_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_36284_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36284 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36284 | HTTPS FTP |
-Related structure data
Related structure data | 8jhqMC 8jhrC 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_36284.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SPNS2 fusion full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: SPNS2 fusion half B map
File | emd_36284_half_map_1.map | ||||||||||||
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Annotation | SPNS2 fusion half B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SPNS2 fusion half A map
File | emd_36284_half_map_2.map | ||||||||||||
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Annotation | SPNS2 fusion half A map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPNS2 fused with PGS
Entire | Name: SPNS2 fused with PGS |
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Components |
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-Supramolecule #1: SPNS2 fused with PGS
Supramolecule | Name: SPNS2 fused with PGS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase
Macromolecule | Name: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase 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: 82.08993 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKL EVLFQGPGSM MCLECASAAA GGAEEEEADA ERRRRRRGAQ RGAGGSGCCG ARGAGGAGVS AAGDEVQTLS GSVRRAPTG PPGTPGTPGC AATAKGPGAQ QPKPASLGRG RGAAAAILSL GNVLNYLDRY TVAGVLLDIQ QHFGVKDRGA G LLQSVFIC ...String: MDYKDDDDKL EVLFQGPGSM MCLECASAAA GGAEEEEADA ERRRRRRGAQ RGAGGSGCCG ARGAGGAGVS AAGDEVQTLS GSVRRAPTG PPGTPGTPGC AATAKGPGAQ QPKPASLGRG RGAAAAILSL GNVLNYLDRY TVAGVLLDIQ QHFGVKDRGA G LLQSVFIC SFMVAAPIFG YLGDRFNRKV ILSCGIFFWS AVTFSSSFIP QQYFWLLVLS RGLVGIGEAS YSTIAPTIIG DL FGIDCSF WNESYLTGSR DERKKSLLSK FGMDEGVTFM FIGRFDRGQK GVDVLLKAIE ILSSKKEFQE MRFIIIGKGD PEL EGWARS LEEKHGNVKV ITEMLSREFV RELYGSVDFV IIPSYFEPFG LVALEAMCLG AIPIASAVGG LRDIITNETG ILVK AGDPG ELANAILKAL ELSRSDLSKF RENCKKRAMS FSTKNTRTLM LSVFYFAIPL GSGLGYITGS SVKQAAGDWH WALRV SPVL GMITGTLILI LVPATKRGHA DQLGDQLKAR TSWLRDMKAL IRNRSYVFSS LATSAVSFAT GALGMWIPLY LHRAQV VQK TAETCNSPPC GAKDSLIFGA ITCFTGFLGV VTGAGATRWC RLKTQRADPL VCAVGMLGSA IFICLIFVAA KSSIVGA YI CIFVGETLLF SNWAITADIL MYVVIPTRRA TAVALQSFTS HLLGDAGSPY LIGFISDLIR QSTKDSPLWE FLSLGYAL M LCPFVVVLGG MFFLATALFF VSDRARAEQQ VNQLAMPPAS VKV UniProtKB: Sphingosine-1-phosphate transporter SPNS2, Glycogen synthase, Sphingosine-1-phosphate transporter SPNS2 |
-Macromolecule #2: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
Macromolecule | Name: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate type: ligand / ID: 2 / Number of copies: 1 / Formula: S1P |
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Molecular weight | Theoretical: 379.472 Da |
Chemical component information | ChemComp-S1P: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 |
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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 K3 (6k x 4k) / Average electron dose: 54.9 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: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 390253 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |