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- PDB-8z9a: Cryo-EM structure of the insect olfactory receptor OR5-Orco heter... -

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Basic information

Entry
Database: PDB / ID: 8z9a
TitleCryo-EM structure of the insect olfactory receptor OR5-Orco heterocomplex from Acyrthosiphon pisum bound with geranyl acetate
Components
  • Odorant receptor, ApisOR5
  • Odorant receptor, ApisOrco
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


olfactory receptor activity / odorant binding / signal transduction / plasma membrane
Similarity search - Function
Olfactory receptor, insect / 7tm Odorant receptor
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / : / Odorant receptor / Odorant receptor
Similarity search - Component
Biological speciesAcyrthosiphon pisum (pea aphid)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, Y.D. / Qiu, L. / Guan, Z.Y. / Wang, Q. / Wang, G.R. / Yin, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: Structural basis for odorant recognition of the insect odorant receptor OR-Orco heterocomplex.
Authors: Yidong Wang / Liang Qiu / Bing Wang / Zeyuan Guan / Zhi Dong / Jie Zhang / Song Cao / Lulu Yang / Bo Wang / Zhou Gong / Liwei Zhang / Weihua Ma / Zhu Liu / Delin Zhang / Guirong Wang / Ping Yin /
Abstract: Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant ...Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant receptor co-receptor (Orco). In this work, we report structures of the OR5-Orco heterocomplex from the pea aphid alone and bound to its known activating ligand, geranyl acetate. In these structures, three Orco subunits serve as scaffold components that cannot bind the ligand and remain relatively unchanged. Upon ligand binding, the pore-forming helix S7b of OR5 shifts outward from the central pore axis, causing an asymmetrical pore opening for ion influx. Our study provides insights into odorant recognition and channel gating of the OR-Orco heterocomplex and offers structural resources to support development of innovative insecticides and repellents for pest control.
History
DepositionApr 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant receptor, ApisOrco
B: Odorant receptor, ApisOrco
C: Odorant receptor, ApisOrco
D: Odorant receptor, ApisOR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,93212
Polymers201,2044
Non-polymers5,7278
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Odorant receptor, ApisOrco


Mass: 52916.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acyrthosiphon pisum (pea aphid) / Gene: Orco / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A1S6J137
#2: Protein Odorant receptor, ApisOR5


Mass: 42454.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acyrthosiphon pisum (pea aphid) / Gene: OR5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A1S6J146
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical ChemComp-SOU / [(2E)-3,7-dimethylocta-2,6-dienyl] ethanoate


Mass: 196.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: OR-Orco heterocomplex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Acyrthosiphon pisum (pea aphid)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 7.5 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: classification
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399858 / Symmetry type: POINT

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