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- EMDB-7352: Cryo-EM structure of Orco -

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Basic information

Entry
Database: EMDB / ID: EMD-7352
TitleCryo-EM structure of Orco
Map dataOdorant receptor
Sample
  • Complex: Orco homotetramer bound to four Fab molecules in a detergent micelle
    • Protein or peptide: Odorant receptor
KeywordsOlfactory receptor / Ion channel / Insect / Fab / MEMBRANE PROTEIN
Function / homologyOlfactory receptor, insect / 7tm Odorant receptor / olfactory receptor activity / odorant binding / membrane => GO:0016020 / signal transduction / identical protein binding / plasma membrane / Odorant receptor
Function and homology information
Biological speciesApocrypta bakeri (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsButterwick JA / Kim KH / Walz T / Ruta V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI103171 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of the insect olfactory receptor Orco.
Authors: Joel A Butterwick / Josefina Del Mármol / Kelly H Kim / Martha A Kahlson / Jackson A Rogow / Thomas Walz / Vanessa Ruta /
Abstract: The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion ...The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion channels comprised of a highly conserved co-receptor (Orco) and a divergent odorant receptor (OR) that confers chemical specificity. Here, we present the single-particle cryo-electron microscopy structure of an Orco homomer from the parasitic fig wasp Apocrypta bakeri at 3.5 Å resolution, providing structural insight into this receptor family. Orco possesses a novel channel architecture, with four subunits symmetrically arranged around a central pore that diverges into four lateral conduits that open to the cytosol. The Orco tetramer has few inter-subunit interactions within the membrane and is bound together by a small cytoplasmic anchor domain. The minimal sequence conservation among ORs maps largely to the pore and anchor domain, shedding light on how the architecture of this receptor family accommodates its remarkable sequence diversity and facilitates the evolution of odour tuning.
History
DepositionJan 19, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseAug 22, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c70
  • Surface level: 8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7352.png

Downloads & links

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Map

FileDownload / File: emd_7352.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOdorant receptor
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-9.285572 - 18.670680000000001
Average (Standard dev.)-0.15935563 (±0.6412915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-9.28618.671-0.159

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Supplemental data

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Sample components

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Entire : Orco homotetramer bound to four Fab molecules in a detergent micelle

EntireName: Orco homotetramer bound to four Fab molecules in a detergent micelle
Components
  • Complex: Orco homotetramer bound to four Fab molecules in a detergent micelle
    • Protein or peptide: Odorant receptor

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Supramolecule #1: Orco homotetramer bound to four Fab molecules in a detergent micelle

SupramoleculeName: Orco homotetramer bound to four Fab molecules in a detergent micelle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Apocrypta bakeri (insect)

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Macromolecule #1: Odorant receptor

MacromoleculeName: Odorant receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Apocrypta bakeri (insect)
Molecular weightTheoretical: 53.513238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGRAKFKHQ GLVADLLPNI RVMQGVGHFM FNYYSEGKKF PHRIYCIVTL LLLLLQYGMM AVNLMMESDD VDDLTANTIT MLFFLHPIV KMIYFPVRSK IFYKTLAIWN NPNSHPLFAE SNARFHALAI TKMRRLLFCV AGATIFSVIS WTGITFIEDS V KRITDPET ...String:
GPGRAKFKHQ GLVADLLPNI RVMQGVGHFM FNYYSEGKKF PHRIYCIVTL LLLLLQYGMM AVNLMMESDD VDDLTANTIT MLFFLHPIV KMIYFPVRSK IFYKTLAIWN NPNSHPLFAE SNARFHALAI TKMRRLLFCV AGATIFSVIS WTGITFIEDS V KRITDPET NETTIIPIPR LMIRTFYPFN AMSGAGHVFA LIYQFYYLVI SMAVSNSLDV LFCSWLLFAC EQLQHLKAIM KP LMELSAT LDTVVPNSGE LFKAGSADHL RESQGVQPSG NGDNVLDVDL RGIYSNRQDF TATFRPTAGT TFNGGVGPNG LTK KQEMLV RSAIKYWVER HKHVVRLVTA VGDAYGVALL LHMLTTTITL TLLAYQATKV NGVNVYAATV IGYLLYTLGQ VFLF CIFGN RLIEESSSVM EAAYSCHWYD GSEEAKTFVQ IVCQQCQKAM SISGAKFFTV SLDLFASVLG AVVTYFMVLV QLK

UniProtKB: Odorant receptor

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1221 / Number real images: 53141 / Average exposure time: 0.2 sec. / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53141

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