[English] 日本語
Yorodumi
- EMDB-36421: The cryo-EM structure of insect gustatory receptor Gr64a from Dro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36421
TitleThe cryo-EM structure of insect gustatory receptor Gr64a from Drosophila melanogaster in complex with sucrose
Map data
Sample
  • Organelle or cellular component: gustatory receptor Gr64a
    • Protein or peptide: Gustatory receptor for sugar taste 64a
Keywordsgustatory receptor / Gr64a / sucrose / ligand-gated ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


proboscis extension reflex / sweet taste receptor activity / detection of chemical stimulus involved in sensory perception of taste / taste receptor activity / sensory perception of sweet taste / sensory perception of taste / signal transduction / membrane / plasma membrane
Similarity search - Function
Gustatory receptor / Trehalose receptor
Similarity search - Domain/homology
Gustatory receptor for sugar taste 64a
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMa D / Guo J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
CitationJournal: Science / Year: 2024
Title: Structural basis for sugar perception by gustatory receptors.
Authors: Demin Ma / Meiqin Hu / Xiaotong Yang / Qiang Liu / Fan Ye / Weijie Cai / Yong Wang / Ximing Xu / Shenghai Chang / Ruiying Wang / Wei Yang / Sheng Ye / Nannan Su / Minrui Fan / Haoxing Xu / Jiangtao Guo /
Abstract: Insects rely on a family of seven transmembrane proteins called gustatory receptors (GRs) to encode different taste modalities, such as sweet and bitter. We report structures of sweet taste ...Insects rely on a family of seven transmembrane proteins called gustatory receptors (GRs) to encode different taste modalities, such as sweet and bitter. We report structures of sweet taste receptors GR43a and GR64a in the apo and sugar-bound states. Both GRs form tetrameric sugar-gated cation channels composed of one central pore domain (PD) and four peripheral ligand-binding domains (LBDs). Whereas GR43a is specifically activated by the monosaccharide fructose that binds to a narrow pocket in LBDs, disaccharides sucrose and maltose selectively activate GR64a by binding to a larger and flatter pocket in LBDs. Sugar binding to LBDs induces local conformational changes, which are subsequently transferred to the PD to cause channel opening. Our studies reveal a structural basis for sugar recognition and activation of GRs.
History
DepositionJun 4, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_36421.png

Downloads & links

-
Map

FileDownload / File: emd_36421.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.0079
Minimum - Maximum-0.04171386 - 0.08406882
Average (Standard dev.)0.000004516194 (±0.003059009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36421_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36421_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : gustatory receptor Gr64a

EntireName: gustatory receptor Gr64a
Components
  • Organelle or cellular component: gustatory receptor Gr64a
    • Protein or peptide: Gustatory receptor for sugar taste 64a

-
Supramolecule #1: gustatory receptor Gr64a

SupramoleculeName: gustatory receptor Gr64a / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Gustatory receptor for sugar taste 64a

MacromoleculeName: Gustatory receptor for sugar taste 64a / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 54.66825 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG GSSGGVDMKG PNLNFRKTPS KDNGVKQVES LARPETPPPK FVEDSNLEFN VLASEKLPNY TNLDLFHRAV FPFMFLAQC VAIMPLVGIR ESNPRRVRFA YKSIPMFVTL IFMIATSILF LSMFTHLLKI GITAKNFVGL VFFGCVLSAY V VFIRLAKK ...String:
MWSHPQFEKG GSSGGVDMKG PNLNFRKTPS KDNGVKQVES LARPETPPPK FVEDSNLEFN VLASEKLPNY TNLDLFHRAV FPFMFLAQC VAIMPLVGIR ESNPRRVRFA YKSIPMFVTL IFMIATSILF LSMFTHLLKI GITAKNFVGL VFFGCVLSAY V VFIRLAKK WPAVVRIWTR TEIPFTKPPY EIPKRNLSRR VQLAALAIIG LSLGEHALYQ VSAILSYTRR IQMCANITTV PS FNNYMQT NYDYVFQLLP YSPIIAVLIL LINGACTFVW NYMDLFIMMI SKGLSYRFEQ ITTRIRKLEH EEVCESVFIQ IRE HYVKMC ELLEFVDSAM SSLILLSCVN NLYFVCYQLL NVFNKLRWPI NYIYFWYSLL YLIGRTAFVF LTAADINEES KRGL GVLRR VSSRSWCVEV ERLIFQMTTQ TVALSGKKFY FLTRRLLFGM AGTIVTYELV LLQFDEPNRR KGLQPLCA

UniProtKB: Gustatory receptor for sugar taste 64a

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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: 1.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 632430

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more