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- EMDB-36285: Cryo-EM structure of human S1P transporter SPNS2 bound with an in... -

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Basic information

Entry
Database: EMDB / ID: EMD-36285
TitleCryo-EM structure of human S1P transporter SPNS2 bound with an inhibitor 16d
Map dataSPNS2 wild type full map
Sample
  • Complex: Wild type SPNS2
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine
KeywordsTranspoter / 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 / 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
Protein spinster-like / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Sphingosine-1-phosphate transporter SPNS2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsPang B / Yu LY / Ren RB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMay 25, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36285.png

Downloads & links

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Map

FileDownload / File: emd_36285.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSPNS2 wild type full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-1.5618533 - 2.5503972
Average (Standard dev.)-0.0017551 (±0.047829434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SPNS2 wild type half B map

Fileemd_36285_half_map_1.map
AnnotationSPNS2 wild type half B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SPNS2 wild type half A map

Fileemd_36285_half_map_2.map
AnnotationSPNS2 wild type half A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wild type SPNS2

EntireName: Wild type SPNS2
Components
  • Complex: Wild type SPNS2
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine

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Supramolecule #1: Wild type SPNS2

SupramoleculeName: Wild type SPNS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sphingosine-1-phosphate transporter SPNS2

MacromoleculeName: Sphingosine-1-phosphate transporter SPNS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.62193 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HSGDEVDAGS GHMMCLECAS AAAGGAEEEE ADAERRRRRR GAQRGAGGSG CCGARGAGGA GVSAAGDEVQ TLSGSVRRA PTGPPGTPGT PGCAATAKGP GAQQPKPASL GRGRGAAAAI LSLGNVLNYL DRYTVAGVLL DIQQHFGVKD R GAGLLQSV ...String:
MHHHHHHHHH HSGDEVDAGS GHMMCLECAS AAAGGAEEEE ADAERRRRRR GAQRGAGGSG CCGARGAGGA GVSAAGDEVQ TLSGSVRRA PTGPPGTPGT PGCAATAKGP GAQQPKPASL GRGRGAAAAI LSLGNVLNYL DRYTVAGVLL DIQQHFGVKD R GAGLLQSV FICSFMVAAP IFGYLGDRFN RKVILSCGIF FWSAVTFSSS FIPQQYFWLL VLSRGLVGIG EASYSTIAPT II GDLFTKN TRTLMLSVFY FAIPLGSGLG YITGSSVKQA AGDWHWALRV SPVLGMITGT LILILVPATK RGHADQLGDQ LKA RTSWLR DMKALIRNRS YVFSSLATSA VSFATGALGM WIPLYLHRAQ VVQKTAETCN SPPCGAKDSL IFGAITCFTG FLGV VTGAG ATRWCRLKTQ RADPLVCAVG MLGSAIFICL IFVAAKSSIV GAYICIFVGE TLLFSNWAIT ADILMYVVIP TRRAT AVAL QSFTSHLLGD AGSPYLIGFI SDLIRQSTKD SPLWEFLSLG YALMLCPFVV VLGGMFFLAT ALFFVSDRAR AEQQVN QLA MPPASVKV

UniProtKB: Sphingosine-1-phosphate transporter SPNS2

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Macromolecule #2: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine

MacromoleculeName: 3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine
type: ligand / ID: 2 / Number of copies: 1 / Formula: YUX
Molecular weightTheoretical: 343.506 Da
Chemical component information

ChemComp-YUX:
3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113289
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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