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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: To Be Published
Title: Cryo-EM structure of the receptor of PL45-Olfr110-Gs complex
Authors: Rong, N.K. / Zhang, M.H. / Yang, F. / Sun, J.P.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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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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