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- EMDB-45879: Consensus olfactory receptor consOR2 bound to S-carvone and in co... -

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Entry
Database: EMDB / ID: EMD-45879
TitleConsensus olfactory receptor consOR2 bound to S-carvone and in complex with mini-Gs trimeric protein (transmembrane domain)
Map dataConsensus olfactory receptor consOR2 bound to S-carvone and in complex with mini-Gs trimeric protein (transmembrane domain)
Sample
  • Complex: consOR2-miniGs complex bound to Nb35
KeywordsOdorant / Olfaction / GPCR / Receptor / SIGNALING PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsBillesboelle CB / Del Torrent CL / Manglik A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC020353 United States
The Vallee Foundation Inc. United States
Chan Zuckerberg Initiative United States
CitationJournal: Nature / Year: 2024
Title: Engineered odorant receptors illuminate the basis of odour discrimination.
Authors: Claire A de March / Ning Ma / Christian B Billesbølle / Jeevan Tewari / Claudia Llinas Del Torrent / Wijnand J C van der Velden / Ichie Ojiro / Ikumi Takayama / Bryan Faust / Linus Li / ...Authors: Claire A de March / Ning Ma / Christian B Billesbølle / Jeevan Tewari / Claudia Llinas Del Torrent / Wijnand J C van der Velden / Ichie Ojiro / Ikumi Takayama / Bryan Faust / Linus Li / Nagarajan Vaidehi / Aashish Manglik / Hiroaki Matsunami /
Abstract: How the olfactory system detects and distinguishes odorants with diverse physicochemical properties and molecular configurations remains poorly understood. Vertebrate animals perceive odours through ...How the olfactory system detects and distinguishes odorants with diverse physicochemical properties and molecular configurations remains poorly understood. Vertebrate animals perceive odours through G protein-coupled odorant receptors (ORs). In humans, around 400 ORs enable the sense of smell. The OR family comprises two main classes: class I ORs are tuned to carboxylic acids whereas class II ORs, which represent most of the human repertoire, respond to a wide variety of odorants. A fundamental challenge in understanding olfaction is the inability to visualize odorant binding to ORs. Here we uncover molecular properties of odorant-OR interactions by using engineered ORs crafted using a consensus protein design strategy. Because such consensus ORs (consORs) are derived from the 17 major subfamilies of human ORs, they provide a template for modelling individual native ORs with high sequence and structural homology. The biochemical tractability of consORs enabled the determination of four cryogenic electron microscopy structures of distinct consORs with specific ligand recognition properties. The structure of a class I consOR, consOR51, showed high structural similarity to the native human receptor OR51E2 and generated a homology model of a related member of the human OR51 family with high predictive power. Structures of three class II consORs revealed distinct modes of odorant-binding and activation mechanisms between class I and class II ORs. Thus, the structures of consORs lay the groundwork for understanding molecular recognition of odorants by the OR superfamily.
History
DepositionJul 22, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45879.png

Downloads & links

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Map

FileDownload / File: emd_45879.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus olfactory receptor consOR2 bound to S-carvone and in complex with mini-Gs trimeric protein (transmembrane domain)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å		0.86 Å/pix.
x 288 pix.
= 247.68 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.587
Minimum - Maximum-3.699313 - 6.0811315
Average (Standard dev.)0.0014847183 (±0.06743044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 247.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45879_msk_1.map
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Half map: Half Map A

Fileemd_45879_half_map_1.map
AnnotationHalf Map A
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Half map: Half Map B

Fileemd_45879_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : consOR2-miniGs complex bound to Nb35

EntireName: consOR2-miniGs complex bound to Nb35
Components
  • Complex: consOR2-miniGs complex bound to Nb35

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Supramolecule #1: consOR2-miniGs complex bound to Nb35

SupramoleculeName: consOR2-miniGs complex bound to Nb35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 100 KDa

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131718
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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