7YUB

S1P-bound human SPNS2

PDB DOI: https://doi.org/10.2210/pdb7YUB/pdb
EM Map EMD-34103: 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 PDBTMMemProtMD

Deposited: 2022-08-17 Released: 2023-09-06
Deposition Author(s): He, Y., Duan, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00913-0
Primary Citation of Related Structures:
7YUB, 7YUD, 7YUF, 8KAE

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.

Macromolecule Content

Total Structure Weight: 122.51 kDa
Atom Count: 7,610
Modelled Residue Count: 997
Deposited Residue Count: 1,139
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NbFab-H-chain	A [auth H]	246	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NbFab-L-chain	B [auth L]	216	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tc-Nb8	C [auth N]	128	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine-1-phosphate transporter SPNS2	D [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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IVW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S1P Query on S1P Download Ideal Coordinates CCD File SDF format, chain E [auth R] MOL2 format, chain E [auth R] mmCIF format, chain E [auth R]	E [auth R]	(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate C₁₈ H₃₈ N O₅ P DUYSYHSSBDVJSM-KRWOKUGFSA-N		Interactions Focus chain E [auth R] Interactions & Density Focus chain E [auth R]