7EW3

Cryo-EM structure of S1P-bound Sphingosine 1-phosphate receptor 3 in complex with Gi protein

PDB DOI: https://doi.org/10.2210/pdb7EW3/pdb
EM Map EMD-31346: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-05-24 Released: 2021-09-29
Deposition Author(s): Zhao, C., Wang, W., Wang, H.L., Shao, Z.H.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into sphingosine-1-phosphate recognition and ligand selectivity of S1PR3-Gi signaling complexes.

Zhao, C., Cheng, L., Wang, W., Wang, H., Luo, Y., Feng, Y., Wang, X., Fu, H., Cai, Y., Yang, S., Fu, P., Yan, W., Shao, Z.

(2022) Cell Res 32: 218-221

PubMed: 34545189 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00567-w
Primary Citation of Related Structures:
7EW2, 7EW3, 7EW4

Organizational Affiliation

Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

Macromolecule Content

Total Structure Weight: 163.9 kDa
Atom Count: 9,072
Modelled Residue Count: 1,149
Deposited Residue Count: 1,459
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	356	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 3	D [auth R]	412	Homo sapiens	Mutation(s): 0 Gene Names: S1PR3, EDG3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q99500 (Homo sapiens) Explore Q99500 Go to UniProtKB: Q99500
PHAROS: Q99500 GTEx: ENSG00000213694
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99500
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFV16	E [auth S]	266	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S1P (Subject of Investigation/LOI) Query on S1P Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	F [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 F [auth R] Interactions & Density Focus chain F [auth R]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain G [auth R] SDF format, chain H [auth R] SDF format, chain I [auth R] SDF format, chain J [auth R] MOL2 format, chain G [auth R] MOL2 format, chain H [auth R] MOL2 format, chain I [auth R] MOL2 format, chain J [auth R] mmCIF format, chain G [auth R] mmCIF format, chain H [auth R] mmCIF format, chain I [auth R] mmCIF format, chain J [auth R]	G [auth R], H [auth R], I [auth R], J [auth R]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Interactions & Density Focus chain G [auth R] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R]

Binding Affinity Annotations
ID	Source	Binding Affinity
S1P	BindingDB: 7EW3	IC50: min: 0.04, max: 0.66 (nM) from 4 assay(s)
S1P	BindingDB: 7EW3	EC50: min: 0.2, max: 79 (nM) from 11 assay(s)