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- EMDB-42629: Structure of the insect gustatory receptor Gr9 from Bombyx mori i... -

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Basic information

Entry
Database: EMDB / ID: EMD-42629
TitleStructure of the insect gustatory receptor Gr9 from Bombyx mori in complex with D-fructose
Map data
Sample
  • Complex: Homotetramer of Gr9 bound to D-fructose
    • Protein or peptide: Gustatory receptor
  • Ligand: beta-D-fructopyranose
  • Ligand: beta-D-fructofuranose
KeywordsGustatory receptor / Ion channel / Sugar-binding / Fructose / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology7TM chemoreceptor / 7tm Chemosensory receptor / sensory perception of taste / signal transduction / plasma membrane / Gustatory receptor
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGomes JV / Butterwick JA
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2024
Title: The molecular basis of sugar detection by an insect taste receptor.
Authors: João Victor Gomes / Shivinder Singh-Bhagania / Matthew Cenci / Carlos Chacon Cordon / Manjodh Singh / Joel A Butterwick /
Abstract: Animals crave sugars because of their energy potential and the pleasurable sensation of tasting sweetness. Yet all sugars are not metabolically equivalent, requiring mechanisms to detect and ...Animals crave sugars because of their energy potential and the pleasurable sensation of tasting sweetness. Yet all sugars are not metabolically equivalent, requiring mechanisms to detect and differentiate between chemically similar sweet substances. Insects use a family of ionotropic gustatory receptors to discriminate sugars, each of which is selectively activated by specific sweet molecules. Here, to gain insight into the molecular basis of sugar selectivity, we determined structures of Gr9, a gustatory receptor from the silkworm Bombyx mori (BmGr9), in the absence and presence of its sole activating ligand, D-fructose. These structures, along with structure-guided mutagenesis and functional assays, illustrate how D-fructose is enveloped by a ligand-binding pocket that precisely matches the overall shape and pattern of chemical groups in D-fructose. However, our computational docking and experimental binding assays revealed that other sugars also bind BmGr9, yet they are unable to activate the receptor. We determined the structure of BmGr9 in complex with one such non-activating sugar, L-sorbose. Although both sugars bind a similar position, only D-fructose is capable of engaging a bridge of two conserved aromatic residues that connects the pocket to the pore helix, inducing a conformational change that allows the ion-conducting pore to open. Thus, chemical specificity does not depend solely on the selectivity of the ligand-binding pocket, but it is an emergent property arising from a combination of receptor-ligand interactions and allosteric coupling. Our results support a model whereby coarse receptor tuning is derived from the size and chemical characteristics of the pocket, whereas fine-tuning of receptor activation is achieved through the selective engagement of an allosteric pathway that regulates ion conduction.
History
DepositionNov 4, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42629.png

Downloads & links

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Map

FileDownload / File: emd_42629.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-3.957185 - 6.586952
Average (Standard dev.)0.0033988033 (±0.10191588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42629_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer of Gr9 bound to D-fructose

EntireName: Homotetramer of Gr9 bound to D-fructose
Components
  • Complex: Homotetramer of Gr9 bound to D-fructose
    • Protein or peptide: Gustatory receptor
  • Ligand: beta-D-fructopyranose
  • Ligand: beta-D-fructofuranose

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Supramolecule #1: Homotetramer of Gr9 bound to D-fructose

SupramoleculeName: Homotetramer of Gr9 bound to D-fructose / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bombyx mori (domestic silkworm)

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Macromolecule #1: Gustatory receptor

MacromoleculeName: Gustatory receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Molecular weightTheoretical: 50.67707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGRAPPSPD LRADEPKTPC LVGGAHAFIL KISSFCGLAP LRFEPRSQEY AVTISKGKCF YSYILVTFLV ICTIYGLVAE IGVGVEKSV RMSSRMSQVV SACDILVVAV TAGVGVYGAP ARMRTMLSYM ENIVAVDREL GRHHSAATER KLCALLLLIL L SFTILLVD ...String:
GPGRAPPSPD LRADEPKTPC LVGGAHAFIL KISSFCGLAP LRFEPRSQEY AVTISKGKCF YSYILVTFLV ICTIYGLVAE IGVGVEKSV RMSSRMSQVV SACDILVVAV TAGVGVYGAP ARMRTMLSYM ENIVAVDREL GRHHSAATER KLCALLLLIL L SFTILLVD DFCFYAMQAG KTGRQWEIVT NYAGFYFLWY IVMVLELQFA FTALSLRARL KLFNEALNVT ASQVCKPVKK PK NSQLSVY ATSVRPVSCK RENVIVETIR VRDKDDAFVM MKTADGVPCL QVPPCEAVGR LSRMRCTLCE VTRHIADGYG LPL VIILMS TLLHLIVTPY FLIMEIIVST HRLHFLVLQF LWCTTHLIRM LVVVEPCHYT IREGKRTEDI LCRLMTLAPH GGVL SSRLE VLSRLLMLQN ISYSPLGMCT LDRPLMVTVL GAVTTYLVIL IQFQRYDS

UniProtKB: Gustatory receptor

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Macromolecule #2: beta-D-fructopyranose

MacromoleculeName: beta-D-fructopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: BDF
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BDF:
beta-D-fructopyranose / Fructose

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Macromolecule #3: beta-D-fructofuranose

MacromoleculeName: beta-D-fructofuranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: FRU
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-FRU:
beta-D-fructofuranose / Fructose

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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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307715
FSC plot (resolution estimation)

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