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- EMDB-65276: The structure of DbOR67d-DbOrco in the cVA-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-65276
TitleThe structure of DbOR67d-DbOrco in the cVA-bound state
Map data
Sample
  • Complex: The structure of DbOR67d-DbOrco in the cVA-bound state
    • Protein or peptide: odorant receptor 67d-like in Drosophila bipectinata
    • Protein or peptide: odorant receptor coreceptor in Drosophila bipectinata
  • Ligand: (Z)-OCTADEC-11-ENYL ACETATE
KeywordsOdorant Receptor / Complex / channel / MEMBRANE PROTEIN
Biological speciesDrosophila bipectinata (fry)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65276.png

Downloads & links

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Map

FileDownload / File: emd_65276.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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: 0.02
Minimum - Maximum-0.059516795 - 0.096714415
Average (Standard dev.)0.000044992677 (±0.0039640423)
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_65276_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65276_half_map_2.map
Projections & Slices
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Sample components

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Entire : The structure of DbOR67d-DbOrco in the cVA-bound state

EntireName: The structure of DbOR67d-DbOrco in the cVA-bound state
Components
  • Complex: The structure of DbOR67d-DbOrco in the cVA-bound state
    • Protein or peptide: odorant receptor 67d-like in Drosophila bipectinata
    • Protein or peptide: odorant receptor coreceptor in Drosophila bipectinata
  • Ligand: (Z)-OCTADEC-11-ENYL ACETATE

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Supramolecule #1: The structure of DbOR67d-DbOrco in the cVA-bound state

SupramoleculeName: The structure of DbOR67d-DbOrco in the cVA-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila bipectinata (fry)

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Macromolecule #1: odorant receptor 67d-like in Drosophila bipectinata

MacromoleculeName: odorant receptor 67d-like in Drosophila bipectinata / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila bipectinata (fry)
Molecular weightTheoretical: 45.317023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKLNTKLTP VDRYLRIIKV IRFFVGFCGN DVANPNFKMW WLTYLVLSAI GLFYACTGYT IYRGVVIDGD LTIILQAMAM VGSATQGLT KLLVTANLAP LLRHIQYSYE DIYREYGAKG GEYTECLERR IRITWRLMLS FLCPCLMSMV CIVSFPIFYL V VYKKKIMV ...String:
MSKLNTKLTP VDRYLRIIKV IRFFVGFCGN DVANPNFKMW WLTYLVLSAI GLFYACTGYT IYRGVVIDGD LTIILQAMAM VGSATQGLT KLLVTANLAP LLRHIQYSYE DIYREYGAKG GEYTECLERR IRITWRLMLS FLCPCLMSMV CIVSFPIFYL V VYKKKIMV MQFLMPLIDE NTDGGYMILS AVHVGLIAFG GFGNYGGDMY LFLFVTNLTL IKDIFCIKIK ELNEVVLKRT EY EQMRLLL FDLVAWHQKY QNILLTTRRI YSIVLFVQLS TTCMSMLCTI ACVFLHVWPA APIYLLYAGT MLYAFCGLGT AVE ISNDAL MREIYSGCLW YELPVKEEKI IVLMLAKAQT ESYLTAANMW PLSMNTALQL TKGMYSFTMM MLTYLGMEK

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Macromolecule #2: odorant receptor coreceptor in Drosophila bipectinata

MacromoleculeName: odorant receptor coreceptor in Drosophila bipectinata / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Drosophila bipectinata (fry)
Molecular weightTheoretical: 53.974578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTTSMQPSKY TGLVADLMPN IKAMKYSGLF MHNFTGGSAF VKKVYSSVHL VLLLLQFVFI LVNMALNAEE VNELSGNTIT TLFFTHCIT KFIYLAVNQK NFYRTLNIWN QVNTHPLFAE SDARYHSIAL AKMRKLFFLV MLTTVASATA WTTITFFGDS V KMVVDHET ...String:
MTTSMQPSKY TGLVADLMPN IKAMKYSGLF MHNFTGGSAF VKKVYSSVHL VLLLLQFVFI LVNMALNAEE VNELSGNTIT TLFFTHCIT KFIYLAVNQK NFYRTLNIWN QVNTHPLFAE SDARYHSIAL AKMRKLFFLV MLTTVASATA WTTITFFGDS V KMVVDHET NSSVPVEIPR LPIKSFYPWN AGHGIFYMIS FAFQIYYILF SMIHSNLCDV MFCSWLIFAC EQLQHLKGIM KP LMELSAS LDTYRPNSAA LFRSLSANSK SELIHNEEKD PGADMDMSGV YSSKADWGAQ FRAPSTLQSF GGNGGIVNGA NPN GLTKKQ EMMVRSAIKY WVERHKHVVR LVAAIGDTYG AALLLHMLTS TIKLTLLAYQ ATKITGVNVY AFTVIGYLGY ALAQ VFHFC IFGNRLIEES SSVMEAAYSC HWYDGSEEAK TFVQIVCQQC QKAMSISGAK FFTVSLDLFA SVLGAVVTYF MVLVQ LK

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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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 62395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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