[English] 日本語
Yorodumi
- EMDB-36284: Cryo-EM structure of human S1P transporter SPNS2 bound with S1P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36284
TitleCryo-EM structure of human S1P transporter SPNS2 bound with S1P
Map dataSPNS2 fusion full map
Sample
  • Complex: SPNS2 fused with PGS
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
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 / glycogen (starch) synthase 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 / glycogen (starch) synthase 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 / sensory perception of sound / bone development / endosome membrane / membrane / plasma membrane / cytosol
Similarity search - Function
Protein spinster-like / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / 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 / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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

-
Structure visualization

Supplemental images

emd_36284.png

Downloads & links

-
Map

FileDownload / File: emd_36284.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSPNS2 fusion full map
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.93918955 - 1.6122469
Average (Standard dev.)0.0011574641 (±0.029732652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: SPNS2 fusion half B map

Fileemd_36284_half_map_1.map
AnnotationSPNS2 fusion half B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: SPNS2 fusion half A map

Fileemd_36284_half_map_2.map
AnnotationSPNS2 fusion half A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SPNS2 fused with PGS

EntireName: SPNS2 fused with PGS
Components
  • Complex: SPNS2 fused with PGS
    • Protein or peptide: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase
  • Ligand: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

-
Supramolecule #1: SPNS2 fused with PGS

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

-
Macromolecule #1: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase

MacromoleculeName: Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.08993 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

MacromoleculeName: (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
type: ligand / ID: 2 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 390253
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more