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Open data
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Basic information
Entry | Database: PDB / ID: 7yud | ||||||
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Title | FTY720p-bound human SPNS2 | ||||||
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![]() | MEMBRANE PROTEIN / transporter | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | synthetic construct (others)![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||
![]() | He, Y. / Duan, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 157.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34104MC ![]() 7yubC ![]() 7yufC ![]() 8kaeC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Antibody , 4 types, 4 molecules HLNK
#1: Antibody | Mass: 26644.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Antibody | Mass: 23389.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
#3: Antibody | Mass: 14001.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Antibody | Mass: 13764.110 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Non-polymers , 2 types, 2 molecules R![](data/chem/img/J89.gif)
![](data/chem/img/J89.gif)
#4: Protein | Mass: 58096.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: Chemical | ChemComp-J89 / ( |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: SPNS2 nanobody complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 362400 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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