8KAE | pdb_00008kae

16d-bound human SPNS2

• PDB DOI: https://doi.org/10.2210/pdb8KAE/pdb
• EM Map EMD-37008: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct, Lama glama, Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2023-08-03 Released: 2024-01-03 
• Deposition Author(s): He, Y., Duan, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of Sphingosine-1-phosphate transport via human SPNS2.

Duan, Y., Leong, N.C.P., Zhao, J., Zhang, Y., Nguyen, D.T., Ha, H.T.T., Wang, N., Xia, R., Xu, Z., Ma, Z., Qian, Y., Yin, H., Zhu, X., Zhang, A., Guo, C., Xia, Y., Nguyen, L.N., He, Y.

(2024) Cell Res 34: 177-180

• PubMed: 38123825 
• DOI: https://doi.org/10.1038/s41422-023-00913-0
• Primary Citation Related Structures: 
  7YUB, 7YUD, 7YUF, 8KAE

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Organizational Affiliation: 
• Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China.
Life Sciences Institute, Immunology Programme, National University of Singapore, Singapore, Singapore.
Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. [e-mail].
Life Sciences Institute, Immunology Programme, National University of Singapore, Singapore, Singapore. [e-mail].
Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. [e-mail].
Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore. [e-mail].
Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 136.24 kDa 
• Atom Count: 8,440 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,265 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NbFab-H chain	A [auth H]	246	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-Fab nb	B [auth K]	126	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NbFab chain L	C [auth L]	216	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tc-nb 8	D [auth N]	128	Lama glama	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine-1-phosphate transporter SPNS2	E [auth R]	549	Homo sapiens	Mutation(s): 0  Gene Names: SPNS2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YUX	F [auth R]	3-[3-(4-decylphenyl)-1,2,4-oxadiazol-5-yl]propan-1-amine C21 H33 N3 O VLTITRMWGPJCFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-03 
Deposition Author(s): He, Y., Duan, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32070048

Revision History  

• Version 1.0: 2024-01-03
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection