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- EMDB-63175: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63175
TitleCryo-EM structure of the receptor of PL45-Olfr110-Gs complex
Map data
Sample
  • Complex: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
    • Protein or peptide: Olfactory receptor
  • Ligand: methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate
KeywordsOlfr110 / receptor / MEMBRANE PROTEIN
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
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRong NK / Zhang MH / Yang F / Sun JP
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63175.png

Downloads & links

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Map

FileDownload / File: emd_63175.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å		0.92 Å/pix.
x 256 pix.
= 235.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.56
Minimum - Maximum-0.12559775 - 24.513152999999999
Average (Standard dev.)-0.02662061 (±0.3094191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63175_msk_1.map
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Half map: #2

Fileemd_63175_half_map_1.map
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Half map: #1

Fileemd_63175_half_map_2.map
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Sample components

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

EntireName: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
Components
  • Complex: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
    • Protein or peptide: Olfactory receptor
  • Ligand: methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate

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Supramolecule #1: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex

SupramoleculeName: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Olfactory receptor

MacromoleculeName: Olfactory receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 35.788172 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGKNQTAPS EFIILGFDHL NELQYLLFTI FFLTYICTLG GNVFIIVVTI ADSHLHTPMY YFLGNLALID ICYTTTNVPQ MMVHLLSEK KIISYGGCVT QLFAFIFFVG SECLLLAAMA YDRYIAICKP LRYSFIMNKA LCSWLAASCW TGGFLNSVLH T VLTFHLPF ...String:
MEGKNQTAPS EFIILGFDHL NELQYLLFTI FFLTYICTLG GNVFIIVVTI ADSHLHTPMY YFLGNLALID ICYTTTNVPQ MMVHLLSEK KIISYGGCVT QLFAFIFFVG SECLLLAAMA YDRYIAICKP LRYSFIMNKA LCSWLAASCW TGGFLNSVLH T VLTFHLPF CGNNQINYFF CDIPPLLILS CGDTSLNELA LLSIGILIGW TPFLCVILSY LYIISTILRI RSSEGRHKAF ST CASHLLI VILYYGSAIF TYVRPISSYS LEKDRLISVL YSVVTPMLNP VIYTLRNKDI KEAVKAIGRK WQPPVFSSDI

UniProtKB: Olfactory receptor

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Macromolecule #2: methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate

MacromoleculeName: methyl (9R,10E,12E)-9-methoxyoctadeca-10,12-dienoate / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EKK
Molecular weightTheoretical: 324.498 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 168745
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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