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- EMDB-65272: The structure of DmOR67d-DmOrco in the cVA-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-65272
TitleThe structure of DmOR67d-DmOrco in the cVA-bound state
Map data
Sample
  • Complex: The structure of DmOR67d-DmOrco in the cVA-bound state
    • Protein or peptide: Odorant receptor 67d
    • Protein or peptide: Odorant receptor coreceptor
  • Ligand: (Z)-OCTADEC-11-ENYL ACETATE
KeywordsOdorant Receptor / Complex / channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


detection of pheromone / ionotropic olfactory receptor activity / sensory dendrite / olfactory receptor activity / response to pheromone / courtship behavior / detection of chemical stimulus involved in sensory perception of smell / olfactory behavior / odorant binding / cation channel complex ...detection of pheromone / ionotropic olfactory receptor activity / sensory dendrite / olfactory receptor activity / response to pheromone / courtship behavior / detection of chemical stimulus involved in sensory perception of smell / olfactory behavior / odorant binding / cation channel complex / behavioral response to ethanol / intracellularly gated calcium channel activity / coreceptor activity / dendrite membrane / sensory perception of smell / regulation of protein localization / calmodulin binding / cilium / dendrite / signal transduction / protein homodimerization activity / plasma membrane
Similarity search - Function
Olfactory receptor, insect / 7tm Odorant receptor
Similarity search - Domain/homology
Odorant receptor coreceptor / Odorant receptor 67d
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang J / Guo J
Funding support China, 1 items
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: Jiangqin Wang / Chuanyan Yang / Shenghai Chang / Dian Jiao / Jiahao Lin / Xiaotong Yang / Weijie Cai / Demin Ma / Zhong Jie Ding / Jia Huang / Jianhua Huang / Minrui Fan / Meiqin Hu / Yong ...Authors: Jiangqin Wang / Chuanyan Yang / Shenghai Chang / Dian Jiao / Jiahao Lin / Xiaotong Yang / Weijie Cai / Demin Ma / Zhong Jie Ding / Jia Huang / Jianhua Huang / Minrui Fan / Meiqin Hu / Yong Wang / Haoxing Xu / Nannan Su / Jiangtao Guo /
Abstract: Pheromones mediate intraspecific communication to regulate the physiology and behavior of animals, particularly insects. The detection of pheromones is initiated by the binding of pheromone ...Pheromones mediate intraspecific communication to regulate the physiology and behavior of animals, particularly insects. The detection of pheromones is initiated by the binding of pheromone molecules, e.g., 11-cis-vaccenyl acetate (cVA) in Drosophila, to specific receptor proteins in chemosensory neurons, but the underlying molecular mechanisms remain unclear. Here, we report structures of Drosophila pheromone receptor OR67d-Orco complexes in apo closed, pheromone-bound open, and synthetic agonist VUAA1-bound open conformations. OR67d and Orco assemble into a hetero-tetrameric channel with a 1:3 stoichiometry. In OR67d, the inverted L-shaped cVA or its analog binds into a deep and bent hydrophobic pocket, inducing both local and global conformational changes that lead to an asymmetrical opening of the channel gate. By comparison, VUAA1 binds to Orco instead of OR67d to cause a similar asymmetrical opening. Together, our studies reveal the structural basis for pheromone activation of hetero-tetrameric pheromone receptors.
History
DepositionJul 5, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65272.png

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.20405085 - 0.46361133
Average (Standard dev.)0.0028626607 (±0.021386586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65272_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_65272_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : The structure of DmOR67d-DmOrco in the cVA-bound state

EntireName: The structure of DmOR67d-DmOrco in the cVA-bound state
Components
  • Complex: The structure of DmOR67d-DmOrco in the cVA-bound state
    • Protein or peptide: Odorant receptor 67d
    • Protein or peptide: Odorant receptor coreceptor
  • Ligand: (Z)-OCTADEC-11-ENYL ACETATE

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Supramolecule #1: The structure of DmOR67d-DmOrco in the cVA-bound state

SupramoleculeName: The structure of DmOR67d-DmOrco in the cVA-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Odorant receptor 67d

MacromoleculeName: Odorant receptor 67d / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 45.925602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLKMAKVEPV ERYCKVIRMI RFCVGFCGND VADPNFRMWW LTYAVMAAIA FFFACTGYTI YVGVVINGDL TIILQALAMV GSAVQGLTK LLVTANNASH MREVQNTYED IYREYGSKGD EYAKCLEKRI RITWTLLIGF MLVYIILLGL VITFPIFYLL I LHQKVLVM ...String:
MLKMAKVEPV ERYCKVIRMI RFCVGFCGND VADPNFRMWW LTYAVMAAIA FFFACTGYTI YVGVVINGDL TIILQALAMV GSAVQGLTK LLVTANNASH MREVQNTYED IYREYGSKGD EYAKCLEKRI RITWTLLIGF MLVYIILLGL VITFPIFYLL I LHQKVLVM QFLIPFLDHT TDGGHLILTA AHVILITFGG FGNYGGDMYL FLFVTHVPLI KDIFCVKLTE FNELVMKRND FP KVRAMLC DLLVWHQLYT RMLQTTKKIY SIVLFVQLST TCVGLLCTIS CIFMKAWPAA PLYLLYAAIT LYTFCGLGTL VEN SNEDFL SVIYTNCLWY ELPVKEEKLI IMMLAKAQNE VVLTAADMAP LSMNTALQLT KGIYSFSMML MNYLGRGRWS HPQF EK

UniProtKB: Odorant receptor 67d

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Macromolecule #2: Odorant receptor coreceptor

MacromoleculeName: Odorant receptor coreceptor / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 55.593195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKM TTSMQPSKYT GLVADLMPNI RAMKYSGLFM HNFTGGSAFM KKVYSSVHLV FLLMQFTFIL VNMALNAEEV NELSGNTIT TLFFTHCITK FIYLAVNQKN FYRTLNIWNQ VNTHPLFAES DARYHSIALA KMRKLFFLVM LTTVASATAW T TITFFGDS ...String:
MDYKDDDDKM TTSMQPSKYT GLVADLMPNI RAMKYSGLFM HNFTGGSAFM KKVYSSVHLV FLLMQFTFIL VNMALNAEEV NELSGNTIT TLFFTHCITK FIYLAVNQKN FYRTLNIWNQ VNTHPLFAES DARYHSIALA KMRKLFFLVM LTTVASATAW T TITFFGDS VKMVVDHETN SSIPVEIPRL PIKSFYPWNA SHGMFYMISF AFQIYYVLFS MIHSNLCDVM FCSWLIFACE QL QHLKGIM KPLMELSASL DTYRPNSAAL FRSLSANSKS ELIHNEEKDP GTDMDMSGIY SSKADWGAQF RAPSTLQSFG GNG GGGNGL VNGANPNGLT KKQEMMVRSA IKYWVERHKH VVRLVAAIGD TYGAALLLHM LTSTIKLTLL AYQATKINGV NVYA FTVVG YLGYALAQVF HFCIFGNRLI EESSSVMEAA YSCHWYDGSE EAKTFVQIVC QQCQKAMSIS GAKFFTVSLD LFASV LGAV VTYFMVLVQL K

UniProtKB: Odorant receptor coreceptor

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Macromolecule #3: (Z)-OCTADEC-11-ENYL ACETATE

MacromoleculeName: (Z)-OCTADEC-11-ENYL ACETATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: VA
Molecular weightTheoretical: 310.515 Da
Chemical component information

ChemComp-VA:
(Z)-OCTADEC-11-ENYL ACETATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 196898
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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