8JHQ | pdb_00008jhq

Cryo-EM structure of human S1P transporter SPNS2 bound with S1P

• PDB DOI: https://doi.org/10.2210/pdb8JHQ/pdb
• EM Map EMD-36284: EMDB EMDataResource

• Classification: LIPID TRANSPORT
• Organism(s): Homo sapiens, Pyrococcus abyssi GE5
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2023-05-25 Released: 2024-01-10 
• Deposition Author(s): Pang, B., Yu, L.Y., Ren, R.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of Spns2-facilitated sphingosine-1-phosphate transport.

Pang, B., Yu, L., Li, T., Jiao, H., Wu, X., Wang, J., He, R., Zhang, Y., Wang, J., Hu, H., Dai, W., Chen, L., Ren, R.

(2024) Cell Res 34: 173-176

• PubMed: 38123824 
• DOI: https://doi.org/10.1038/s41422-023-00908-x
• Primary Citation of Related Structures:  
  8JHQ, 8JHR

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Organizational Affiliation: 
• Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.
School of Pharmacy, Second Military Medical University, Shanghai, China.
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China. [e-mail].
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China. [e-mail].
Shanghai Qi Zhi Institute, Shanghai, China. [e-mail].
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China. [e-mail].
Shanghai Qi Zhi Institute, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 82.47 kDa 
• Atom Count: 3,420 
• Modeled Residue Count: 446 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine-1-phosphate transporter SPNS2,GlgA glycogen synthase	A	764	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: SPNS2, PAB2292 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVW8 (Homo sapiens) Explore Q8IVW8  Go to UniProtKB:  Q8IVW8
PHAROS:  Q8IVW8 GTEx:  ENSG00000183018
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8  Go to UniProtKB:  Q9V2J8
UniProt Groups	Q8IVW8Q9V2J8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S1P (Subject of Investigation/LOI)	B [auth A]	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate C18 H38 N O5 P DUYSYHSSBDVJSM-KRWOKUGFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Pang, B., Yu, L.Y., Ren, R.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Structure summary