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- PDB-8z9z: Cryo-EM structure of the insect olfactory receptor OR5-Orco heter... -

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Basic information

Entry
Database: PDB / ID: 8z9z
TitleCryo-EM structure of the insect olfactory receptor OR5-Orco heterocomplex from Acyrthosiphon pisum
Components
  • Odorant receptor, ApisOR5
  • Odorant receptor, ApisOrco
KeywordsMEMBRANE PROTEIN
Function / homologyOlfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / signal transduction / plasma membrane / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Odorant receptor / Odorant receptor
Function and homology information
Biological speciesAcyrthosiphon pisum (pea aphid)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 ligand modulation of insect olfactory receptor OR-Orco heterocomplex
Authors: Wang, Y.D. / Yin, P.
History
DepositionApr 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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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)205,94510
Polymers201,2044
Non-polymers4,7416
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.: 6 / Source method: obtained synthetically / Formula: C44H88NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278564 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212976
ELECTRON MICROSCOPYf_angle_d0.4717571
ELECTRON MICROSCOPYf_dihedral_angle_d8.4511863
ELECTRON MICROSCOPYf_chiral_restr0.0362013
ELECTRON MICROSCOPYf_plane_restr0.0032079

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