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- EMDB-35773: Human Consensus Olfactory Receptor OR52c in Complex with Octanoic... -

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Basic information

Entry
Database: EMDB / ID: EMD-35773
TitleHuman Consensus Olfactory Receptor OR52c in Complex with Octanoic Acid (OCA) and G Protein (G protein-focused map)
Map dataThis is a G protein-focused map of human consensus olfactory receptor OR52c in complex with octanoic Acid (OCA) and G protein. This map was generated with Local refinement tool in cryoSPARC.
Sample
  • Complex: Complex of Consensus Olfactory receptor OR52c in complex with Octanoic acid, G protein and Nanobody 35 (Nb35)
KeywordsOlfactory Receptor / G Protein / MEMBRANE PROTEIN / GPCR / Olfactory GPCR
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChoi CW / Bae J / Choi H-J
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Samsung Science and Technology FoundationSSTF-BA1901-09 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2023
Title: Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family.
Authors: Chulwon Choi / Jungnam Bae / Seonghan Kim / Seho Lee / Hyunook Kang / Jinuk Kim / Injin Bang / Kiheon Kim / Won-Ki Huh / Chaok Seok / Hahnbeom Park / Wonpil Im / Hee-Jung Choi /
Abstract: Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of ...Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52 reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52 demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.
History
DepositionMar 30, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35773.png

Downloads & links

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Map

FileDownload / File: emd_35773.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a G protein-focused map of human consensus olfactory receptor OR52c in complex with octanoic Acid (OCA) and G protein. This map was generated with Local refinement tool in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340.4 Å		0.85 Å/pix.
x 400 pix.
= 340.4 Å		0.85 Å/pix.
x 400 pix.
= 340.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.851 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-3.855546 - 5.018383
Average (Standard dev.)0.0007601868 (±0.090534486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: This is a half B map of the G protein-focused map.

Fileemd_35773_half_map_1.map
AnnotationThis is a half B map of the G protein-focused map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is a half A map of the G protein-focused map.

Fileemd_35773_half_map_2.map
AnnotationThis is a half A map of the G protein-focused map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Consensus Olfactory receptor OR52c in complex with Oct...

EntireName: Complex of Consensus Olfactory receptor OR52c in complex with Octanoic acid, G protein and Nanobody 35 (Nb35)
Components
  • Complex: Complex of Consensus Olfactory receptor OR52c in complex with Octanoic acid, G protein and Nanobody 35 (Nb35)

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Supramolecule #1: Complex of Consensus Olfactory receptor OR52c in complex with Oct...

SupramoleculeName: Complex of Consensus Olfactory receptor OR52c in complex with Octanoic acid, G protein and Nanobody 35 (Nb35)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris(hydroxymethyl)aminomethane
100.0 mMNaClSodium Chloride
0.005 %C47H88O22Lauryl Maltose Neopentyl Glycol
0.0005 %C31H50O4Cholesteryl hemisuccinate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4798 / Average exposure time: 3.05 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 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: OTHER
Details: Initial 3D model was generated with Ab-initio Reconstruction tool in cryoSPARC software.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126896
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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