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- EMDB-34103: S1P-bound human SPNS2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-34103
TitleS1P-bound human SPNS2
Map data
Sample
  • Complex: SPNS2 nanobody complex
    • Protein or peptide: NbFab-H-chain
    • Protein or peptide: NbFab-L-chain
    • Protein or peptide: Tc-Nb8
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
Keywordstransporter / MEMBRANE PROTEIN
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 speciesLama glama (llama) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsHe Y / Duan Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070048 China
CitationJournal: Cell Res / Year: 2024
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
DepositionAug 17, 2022-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34103.png

Downloads & links

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Map

FileDownload / File: emd_34103.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-6.003209 - 9.666055999999999
Average (Standard dev.)0.001554063 (±0.13991098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34103_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34103_half_map_2.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 : SPNS2 nanobody complex

EntireName: SPNS2 nanobody complex
Components
  • Complex: SPNS2 nanobody complex
    • Protein or peptide: NbFab-H-chain
    • Protein or peptide: NbFab-L-chain
    • Protein or peptide: Tc-Nb8
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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Supramolecule #1: SPNS2 nanobody complex

SupramoleculeName: SPNS2 nanobody complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: NbFab-H-chain

MacromoleculeName: NbFab-H-chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.644539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: NbFab-L-chain

MacromoleculeName: NbFab-L-chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.38998 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: Tc-Nb8

MacromoleculeName: Tc-Nb8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.001732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QRQLVESGGG LVQPGGSLRL SCAAPGSRRF DYYTLGWFRQ APGKEREGVS CISTVGGITN YADSVKGRFI ISRDNAKSTV YLQMNSLEP EDTAVYYCAA GREMCAPMML GDYYDMDYWG KGTPVTVSS

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Macromolecule #4: Sphingosine-1-phosphate transporter SPNS2

MacromoleculeName: Sphingosine-1-phosphate transporter SPNS2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.096289 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #5: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

MacromoleculeName: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: S1P
Molecular weightTheoretical: 379.472 Da
Chemical component information

ChemComp-S1P:
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136340
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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