+Open data
-Basic information
Entry | Database: PDB / ID: 8jhq | ||||||
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Title | Cryo-EM structure of human S1P transporter SPNS2 bound with S1P | ||||||
Components | Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase | ||||||
Keywords | LIPID TRANSPORT / Transpoter | ||||||
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) Pyrococcus abyssi (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Pang, B. / Yu, L.Y. / Ren, R.B. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jhq.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jhq.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jhq_validation.pdf.gz | 413.1 KB | Display | wwPDB validaton report |
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Full document | 8jhq_full_validation.pdf.gz | 417.2 KB | Display | |
Data in XML | 8jhq_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 8jhq_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/8jhq ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jhq | HTTPS FTP |
-Related structure data
Related structure data | 36284MC 8jhrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 82089.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Gene: SPNS2, PAB2292 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8IVW8, UniProt: Q9V2J8 |
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#2: Chemical | ChemComp-S1P / ( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SPNS2 fused with PGS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F | ||||||||||||
Buffer solution | pH: 8.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 54.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 390253 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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