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- PDB-9lkd: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex -

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Basic information

Entry
Database: PDB / ID: 9lkd
TitleCryo-EM structure of the receptor of PL45-Olfr110-Gs complex
ComponentsOlfactory receptor
KeywordsMEMBRANE PROTEIN / Olfr110 / receptor
Function / homology
Function and homology information


olfactory receptor activity / detection of chemical stimulus involved in sensory perception of smell / G protein-coupled receptor activity / sensory perception of smell / G protein-coupled receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
: / Olfactory receptor / Olfactory receptor / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / Olfactory receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRong, N.K. / Zhang, M.H. / Yang, F. / Sun, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773704 China
CitationJournal: Cell / Year: 2026
Title: Mechanistic insights into fatty acid odor detection mediated by class II olfactory receptors.
Authors: Xiang Han / Ming-Hui Zhang / Nai-Kang Rong / Kong-Kai Zhu / Yuan Pei / Xiao-Yan Ge / Qi Liu / Huan Lu / Jing Liu / Li-Jun Zhang / Hong-Qiang Bao / Jia-Hao Pi / Lei Fan / Yu Fu / Xu-Hang Shao ...Authors: Xiang Han / Ming-Hui Zhang / Nai-Kang Rong / Kong-Kai Zhu / Yuan Pei / Xiao-Yan Ge / Qi Liu / Huan Lu / Jing Liu / Li-Jun Zhang / Hong-Qiang Bao / Jia-Hao Pi / Lei Fan / Yu Fu / Xu-Hang Shao / Wen-Qi Yan / Xi-He Gao / Ming-Yue Zhang / Lu-Lu Guo / Yan Lu / Shang-Lei Ning / Hua Zhang / Yun-Fei Xu / Xiao-Ya Feng / Jie Cheng / Ming Xia / Qian Li / Xiao Yu / Fan Yang / Jin-Peng Sun /
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 ...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.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Olfactory receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1132
Polymers35,7881
Non-polymers3241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Olfactory receptor


Mass: 35788.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Or5v1, Olfr110 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2RT31
#2: Chemical ChemComp-A1EKK / methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate


Mass: 324.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.875 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
2PHENIX1.18.2_3874model refinement
13cryoSPARC4.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168745 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052013
ELECTRON MICROSCOPYf_angle_d0.9782738
ELECTRON MICROSCOPYf_dihedral_angle_d8.237290
ELECTRON MICROSCOPYf_chiral_restr0.052336
ELECTRON MICROSCOPYf_plane_restr0.012331

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