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- PDB-8vv3: Structure of the insect gustatory receptor Gr9 from Bombyx mori i... -

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Basic information

Entry
Database: PDB / ID: 8vv3
TitleStructure of the insect gustatory receptor Gr9 from Bombyx mori in complex with L-sorbose
ComponentsGustatory receptor
KeywordsTRANSPORT PROTEIN / Gustatory receptor / Ion channel / Sugar-binding / Fructose
Function / homology
Function and homology information


detection of chemical stimulus involved in sensory perception of sweet taste / ionotropic taste receptor activity / ligand-gated monoatomic cation channel activity / monoatomic cation transmembrane transport / signal transduction / plasma membrane
Similarity search - Function
7TM chemoreceptor / 7tm Chemosensory receptor
Similarity search - Domain/homology
alpha-L-sorbopyranose / Gustatory receptor
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsGomes, J.V. / Butterwick, J.A.
Funding support1items
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
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gustatory receptor
B: Gustatory receptor
C: Gustatory receptor
D: Gustatory receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,4298
Polymers202,7084
Non-polymers7214
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gustatory receptor


Mass: 50677.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: Gr9, 100174818 / Production host: Homo sapiens (human) / References: UniProt: B3GTD7
#2: Sugar
ChemComp-SOE / alpha-L-sorbopyranose / alpha-L-sorbose / L-sorbose / sorbose / L-sorbose in pyranose form


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LSorpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-sorbopyranoseCOMMON NAMEGMML 1.0
a-L-SorpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
SorSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homotetramer of Gr9 bound to L-sorbose / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bombyx mori (domestic silkworm)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 920021 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212408
ELECTRON MICROSCOPYf_angle_d0.41316836
ELECTRON MICROSCOPYf_dihedral_angle_d3.0711696
ELECTRON MICROSCOPYf_chiral_restr0.0342076
ELECTRON MICROSCOPYf_plane_restr0.0032024

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