[English] 日本語
Yorodumi- PDB-8jhr: Cryo-EM structure of human S1P transporter SPNS2 bound with an in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jhr | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human S1P transporter SPNS2 bound with an inhibitor 16d | ||||||
Components | Sphingosine-1-phosphate transporter SPNS2 | ||||||
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 / 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 / bone development / sensory perception of sound / endosome membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||
Authors | Pang, B. / Yu, L.Y. / Ren, R.B. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jhr.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jhr.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jhr_validation.pdf.gz | 422.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jhr_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 8jhr_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 8jhr_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/8jhr ftp://data.pdbj.org/pub/pdb/validation_reports/jh/8jhr | HTTPS FTP |
-Related structure data
Related structure data | 36285MC 8jhqC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 60621.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPNS2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IVW8 |
---|---|
#2: Chemical | ChemComp-YUX / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Wild type SPNS2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: sf9 |
Buffer solution | pH: 7 |
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 |
---|---|
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: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113289 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|