9LKD | pdb_00009lkd

Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Mechanistic insights into fatty acid odor detection mediated by class II olfactory receptors.

Han, X.Zhang, M.H.Rong, N.K.Zhu, K.K.Pei, Y.Ge, X.Y.Liu, Q.Lu, H.Liu, J.Zhang, L.J.Bao, H.Q.Pi, J.H.Fan, L.Fu, Y.Shao, X.H.Yan, W.Q.Gao, X.H.Zhang, M.Y.Guo, L.L.Lu, Y.Ning, S.L.Zhang, H.Xu, Y.F.Feng, X.Y.Cheng, J.Xia, M.Li, Q.Yu, X.Yang, F.Sun, J.P.

(2026) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2025.12.018
  • Primary Citation of Related Structures:  
    9LKB, 9LKD, 9WPM

  • PubMed Abstract: 

    Smell is one of the fundamental senses mediated by thousands of odorant receptors (ORs). How hydrophobic and volatile odor molecules are recognized by class II ORs remains elusive. Here, we present cryo-electron microscopy (cryo-EM) structures of class II OR Olfr110 complexed with the unsaturated fatty acid metabolite (UFAM) PL45, Gs, and cons-OR5. The structural study revealed an unusually large hydrophobic pocket accommodating PL45 and the endogenous agonist 12(S)-hydroxyeicosapentaenoic acid (12(S)-HEPE). This pocket is decorated with polar residues and aromatic residue arrays, constituting polar networks and π-π interactions with the natural agonist PL45, respectively. Conserved motifs in the type II OR5 subfamily responsible for ligand recognition are characterized. The inward movement of extracellular loop 3 (ECL3) and an unconventional activation mechanism underlie Olfr110 activation. At the G protein interface, Olfr110 displays common and unique interactions. Overall, we revealed the structural basis of odor recognition and the activation mechanism of class II ORs, which may facilitate drug development targeting these receptors.


  • Organizational Affiliation
    • Shandong Provincial Third Hospital, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; NHC Key Laboratory of Otorhinolaryngology, Qilu hospital and New Cornerstone Science Laboratory, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Olfactory receptorA [auth R]317Mus musculusMutation(s): 0 
Gene Names: Or5v1Olfr110
UniProt
Find proteins for A2RT31 (Mus musculus)
Explore A2RT31 
Go to UniProtKB:  A2RT31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RT31
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EKK (Subject of Investigation/LOI)
Query on A1EKK

Download Ideal Coordinates CCD File 
B [auth R]methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate
C20 H36 O3
TTYSQURQVGCMHK-IOVFVLODSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874
RECONSTRUCTIONcryoSPARC4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81773704

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references
  • Version 1.2: 2026-02-18
    Changes: Data collection, Database references