[English] 日本語
Yorodumi
- EMDB-65274: The structure of DmOR67d-DmOrco in the VUAA1-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65274
TitleThe structure of DmOR67d-DmOrco in the VUAA1-bound state
Map data
Sample
  • Complex: The structure of DmOR67d-DmOrco in the VUAA1-bound state
    • Protein or peptide: Odorant receptor 67d
    • Protein or peptide: Odorant receptor coreceptor
  • Ligand: ~{N}-(4-ethylphenyl)-2-[(4-ethyl-5-pyridin-3-yl-1,2,4-triazol-3-yl)sulfanyl]ethanamide
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: 2.8 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

-
Structure visualization

Supplemental images

emd_65274.png

Downloads & links

-
Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.57713026 - 1.0238502
Average (Standard dev.)0.0038141718 (±0.043441515)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: #3

Fileemd_65274_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_65274_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_65274_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65274_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65274_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The structure of DmOR67d-DmOrco in the VUAA1-bound state

EntireName: The structure of DmOR67d-DmOrco in the VUAA1-bound state
Components
  • Complex: The structure of DmOR67d-DmOrco in the VUAA1-bound state
    • Protein or peptide: Odorant receptor 67d
    • Protein or peptide: Odorant receptor coreceptor
  • Ligand: ~{N}-(4-ethylphenyl)-2-[(4-ethyl-5-pyridin-3-yl-1,2,4-triazol-3-yl)sulfanyl]ethanamide

-
Supramolecule #1: The structure of DmOR67d-DmOrco in the VUAA1-bound state

SupramoleculeName: The structure of DmOR67d-DmOrco in the VUAA1-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
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: 44.512012 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 MNYLG

UniProtKB: Odorant receptor 67d

-
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: 54.465027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTTSMQPSKY TGLVADLMPN IRAMKYSGLF MHNFTGGSAF MKKVYSSVHL VFLLMQFTFI LVNMALNAEE VNELSGNTIT TLFFTHCIT KFIYLAVNQK NFYRTLNIWN QVNTHPLFAE SDARYHSIAL AKMRKLFFLV MLTTVASATA WTTITFFGDS V KMVVDHET ...String:
MTTSMQPSKY TGLVADLMPN IRAMKYSGLF MHNFTGGSAF MKKVYSSVHL VFLLMQFTFI LVNMALNAEE VNELSGNTIT TLFFTHCIT KFIYLAVNQK NFYRTLNIWN QVNTHPLFAE SDARYHSIAL AKMRKLFFLV MLTTVASATA WTTITFFGDS V KMVVDHET NSSIPVEIPR LPIKSFYPWN ASHGMFYMIS FAFQIYYVLF SMIHSNLCDV MFCSWLIFAC EQLQHLKGIM KP LMELSAS LDTYRPNSAA LFRSLSANSK SELIHNEEKD PGTDMDMSGI YSSKADWGAQ FRAPSTLQSF GGNGGGGNGL VNG ANPNGL TKKQEMMVRS AIKYWVERHK HVVRLVAAIG DTYGAALLLH MLTSTIKLTL LAYQATKING VNVYAFTVVG YLGY ALAQV FHFCIFGNRL IEESSSVMEA AYSCHWYDGS EEAKTFVQIV CQQCQKAMSI SGAKFFTVSL DLFASVLGAV VTYFM VLVQ LK

UniProtKB: Odorant receptor coreceptor

-
Macromolecule #3: ~{N}-(4-ethylphenyl)-2-[(4-ethyl-5-pyridin-3-yl-1,2,4-triazol-3-y...

MacromoleculeName: ~{N}-(4-ethylphenyl)-2-[(4-ethyl-5-pyridin-3-yl-1,2,4-triazol-3-yl)sulfanyl]ethanamide
type: ligand / ID: 3 / Number of copies: 3 / Formula: A1ETA
Molecular weightTheoretical: 367.468 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 116983
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more