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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | S1P-bound human SPNS2 | |||||||||
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![]() | transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
![]() | He Y / Duan Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of Sphingosine-1-phosphate transport via human SPNS2. Authors: Yaning Duan / Nancy C P Leong / Jing Zhao / Yu Zhang / Dat T Nguyen / Hoa T T Ha / Na Wang / Ruixue Xia / Zhenmei Xu / Zhengxiong Ma / Yu Qian / Han Yin / Xinyan Zhu / Anqi Zhang / Changyou ...Authors: Yaning Duan / Nancy C P Leong / Jing Zhao / Yu Zhang / Dat T Nguyen / Hoa T T Ha / Na Wang / Ruixue Xia / Zhenmei Xu / Zhengxiong Ma / Yu Qian / Han Yin / Xinyan Zhu / Anqi Zhang / Changyou Guo / Yu Xia / Long N Nguyen / Yuanzheng He / ![]() ![]() | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 80.4 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 801.7 KB | Display | ![]() |
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Full document | ![]() | 801.3 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yubMC ![]() 7yudC ![]() 7yufC ![]() 8kaeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34103_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34103_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SPNS2 nanobody complex
Entire | Name: SPNS2 nanobody complex |
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Components |
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-Supramolecule #1: SPNS2 nanobody complex
Supramolecule | Name: SPNS2 nanobody complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: NbFab-H-chain
Macromolecule | Name: NbFab-H-chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 26.644539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNFSYYSIHW VRQAPGKGLE WVAYISSSSS YTSYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARGYQYWQY HASWYWNGGL DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String: MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNFSYYSIHW VRQAPGKGLE WVAYISSSSS YTSYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARGYQYWQY HASWYWNGGL DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT HHHHHH |
-Macromolecule #2: NbFab-L-chain
Macromolecule | Name: NbFab-L-chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 23.38998 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSDIQMTQSP SSLSASVGDR VTITCRASQS VSSAVAWYQQ KPGKAPKLLI YSASSLYSGV PSRFSGSRSG TDFTLTISSL QPEDFATYY CQQSSSSLIT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: MSDIQMTQSP SSLSASVGDR VTITCRASQS VSSAVAWYQQ KPGKAPKLLI YSASSLYSGV PSRFSGSRSG TDFTLTISSL QPEDFATYY CQQSSSSLIT FGQGTKVEIK RTVAAPSVFI FPPSDSQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #3: Tc-Nb8
Macromolecule | Name: Tc-Nb8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.001732 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QRQLVESGGG LVQPGGSLRL SCAAPGSRRF DYYTLGWFRQ APGKEREGVS CISTVGGITN YADSVKGRFI ISRDNAKSTV YLQMNSLEP EDTAVYYCAA GREMCAPMML GDYYDMDYWG KGTPVTVSS |
-Macromolecule #4: Sphingosine-1-phosphate transporter SPNS2
Macromolecule | Name: Sphingosine-1-phosphate transporter SPNS2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.096289 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL SGSVRRAPTG PPGTPGTPGC AATAKGPGA QQPKPASLGR GRGAAAAILS LGNVLNYLDR YTVAGVLLDI QQHFGVKDRG AGLLQSVFIC SFMVAAPIFG Y LGDRFNRK ...String: MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL SGSVRRAPTG PPGTPGTPGC AATAKGPGA QQPKPASLGR GRGAAAAILS LGNVLNYLDR YTVAGVLLDI QQHFGVKDRG AGLLQSVFIC SFMVAAPIFG Y LGDRFNRK VILSCGIFFW SAVTFSSSFI PQQYFWLLVL SRGLVGIGEA SYSTIAPTII GDLFTKNTRT LMLSVFYFAI PL GSGLGYI TGSSVKQAAG DWHWALRVSP VLGMITGTLI LILVPATKRG HADQLGDQLK ARTSWLRDMK ALIRNRSYVF SSL ATSAVS FATGALGMWI PLYLHRAQVV QKTAETCNSP PCGAKDSLIF GAITCFTGFL GVVTGAGATR WCRLKTQRAD PLVC AVGML GSAIFICLIF VAAKSSIVGA YICIFVGETL LFSNWAITAD ILMYVVIPTR RATAVALQSF TSHLLGDAGS PYLIG FISD LIRQSTKDSP LWEFLSLGYA LMLCPFVVVL GGMFFLATAL FFVSDRARAE QQVNQLAMPP ASVKV UniProtKB: Sphingosine-1-phosphate transporter SPNS2 |
-Macromolecule #5: (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: 5 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |