Human GPR34 -Gi complex bound to S3E-LysoPS, receptor focused

Experimental Data Snapshot

  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Structural basis for lysophosphatidylserine recognition by GPR34.

Izume, T.Kawahara, R.Uwamizu, A.Chen, L.Yaginuma, S.Omi, J.Kawana, H.Hou, F.Sano, F.K.Tanaka, T.Kobayashi, K.Okamoto, H.H.Kise, Y.Ohwada, T.Aoki, J.Shihoya, W.Nureki, O.

(2024) Nat Commun 15: 902-902

  • DOI: https://doi.org/10.1038/s41467-024-45046-z
  • Primary Citation of Related Structures:  
    8XBE, 8XBG, 8XBH, 8XBI

  • PubMed Abstract: 

    GPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron microscopy structures of human GPR34-G i complex bound with one of two ligands bound: either the LysoPS analogue S3E-LysoPS, or M1, a derivative of S3E-LysoPS in which oleic acid is substituted with a metabolically stable aromatic fatty acid surrogate. The ligand-binding pocket is laterally open toward the membrane, allowing lateral entry of lipidic agonists into the cavity. The amine and carboxylate groups of the serine moiety are recognized by the charged residue cluster. The acyl chain of S3E-LysoPS is bent and fits into the L-shaped hydrophobic pocket in TM4-5 gap, and the aromatic fatty acid surrogate of M1 fits more appropriately. Molecular dynamics simulations further account for the LysoPS-regioselectivity of GPR34. Thus, using a series of structural and physiological experiments, we provide evidence that chemically unstable 2-acyl LysoPS is the physiological ligand for GPR34. Overall, we anticipate the present structures will pave the way for development of novel anticancer drugs that specifically target GPR34.

  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable G-protein coupled receptor 34396Homo sapiensMutation(s): 0 
Gene Names: GPR34
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPC5 (Homo sapiens)
Explore Q9UPC5 
Go to UniProtKB:  Q9UPC5
GTEx:  ENSG00000171659 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPC5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KW0 (Subject of Investigation/LOI)
Query on KW0

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[(~{Z})-octadec-9-enoyl]oxy-propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid
C26 H50 N O9 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H05037

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release