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- PDB-9vqu: The structure of DbOR67d-DbOrco in the Z11-bound state -

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Basic information

Entry
Database: PDB / ID: 9vqu
TitleThe structure of DbOR67d-DbOrco in the Z11-bound state
Components
  • OR67d in Drosophila Bipectinata
  • Orco in Drosophila Bipectinata
KeywordsMEMBRANE PROTEIN / Odorant Receptor / Complex / channel
Function / homology:
Function and homology information
Biological speciesDrosophila bipectinata (fry)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, J. / Guo, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
CitationJournal: Cell Res. / Year: 2026
Title: Cryo-EM structures of Drosophila OR67d-Orco complexes reveal insect pheromone sensing mechanism.
Authors: Wang, J. / Yang, C. / Chang, S. / Jiao, D. / Lin, J. / Yang, X. / Cai, W. / Ma, D. / Ding, Z.J. / Huang, J. / Huang, J. / Fan, M. / Hu, M. / Wang, Y. / Xu, H. / Su, N. / Guo, J.
History
DepositionJul 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OR67d in Drosophila Bipectinata
B: Orco in Drosophila Bipectinata
C: Orco in Drosophila Bipectinata
D: Orco in Drosophila Bipectinata
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,5145
Polymers206,1754
Non-polymers3391
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein OR67d in Drosophila Bipectinata


Mass: 44251.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila bipectinata (fry) / Production host: Homo sapiens (human)
#2: Protein Orco in Drosophila Bipectinata


Mass: 53974.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila bipectinata (fry) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-A1ETW / [(~{Z})-icos-11-enyl] ethanoate


Mass: 338.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H42O2 / 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: The structure of DbOR67d-DbOrco in the Z11-bound state
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Drosophila bipectinata (fry)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 594089 / Symmetry type: POINT

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