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- PDB-8v00: AaegOR10 apo structure -

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Basic information

Entry
Database: PDB / ID: 8v00
TitleAaegOR10 apo structure
Components
  • Odorant receptor OR10
  • Odorant receptor Orco
KeywordsMEMBRANE PROTEIN / Mosquito olfactory receptor
Function / homologyOlfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / signal transduction / identical protein binding / plasma membrane / Odorant receptor / Odorant receptor
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
Apocrypta bakeri (insect)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsZhao, J. / del Marmol, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)5R00DC019401 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Structural basis of odor sensing by insect heteromeric odorant receptors.
Authors: Jiawei Zhao / Andy Q Chen / Jaewook Ryu / Josefina Del Mármol /
Abstract: Most insects, including human-targeting mosquitoes, detect odors through odorant-activated ion channel complexes consisting of a divergent odorant-binding subunit (OR) and a conserved co-receptor ...Most insects, including human-targeting mosquitoes, detect odors through odorant-activated ion channel complexes consisting of a divergent odorant-binding subunit (OR) and a conserved co-receptor subunit (Orco). As a basis for understanding how odorants activate these heteromeric receptors, we report here cryo-electron microscopy (cryo-EM) structures of two different heteromeric odorant receptor complexes containing ORs from disease-vector mosquitos or . These structures reveal an unexpected stoichiometry of 1 OR to 3 Orco subunits. Comparison of structures in odorant-bound and unbound states indicates that odorant binding to the sole OR subunit is sufficient to open the channel pore, suggesting a mechanism of OR activation and a conceptual framework for understanding evolution of insect odorant receptor sensitivity.
History
DepositionNov 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Odorant receptor OR10
A: Odorant receptor Orco
B: Odorant receptor Orco
C: Odorant receptor Orco


Theoretical massNumber of molelcules
Total (without water)203,1064
Polymers203,1064
Non-polymers00
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 OR10


Mass: 43491.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: GPRor10 / Production host: Homo sapiens (human) / References: UniProt: Q177X3
#2: Protein Odorant receptor Orco


Mass: 53204.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apocrypta bakeri (insect) / Gene: Or2 / Production host: Homo sapiens (human) / References: UniProt: B0FAQ4

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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

Component
IDNameTypeEntity IDParent-IDSource
1AaegOR10 heterotetramer without ligandCOMPLEXall0MULTIPLE SOURCES
2Aedes aegypti OR10COMPLEX#11RECOMBINANT
3Apocrypta bakeri OrcoCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Aedes aegypti (yellow fever mosquito)7159
43Apocrypta bakeri (insect)490712
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386704 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 55.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004312776
ELECTRON MICROSCOPYf_angle_d0.556517323
ELECTRON MICROSCOPYf_chiral_restr0.03782032
ELECTRON MICROSCOPYf_plane_restr0.00492101
ELECTRON MICROSCOPYf_dihedral_angle_d6.91261724

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