[English] 日本語
Yorodumi
- PDB-8ze2: Drosophila melanogaster gustatory receptor 64a(Gr64a) in Sucrose-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ze2
TitleDrosophila melanogaster gustatory receptor 64a(Gr64a) in Sucrose-bound state
ComponentsGustatory receptor for sugar taste 64a
KeywordsPROTEIN TRANSPORT / gustatory receptors / ion channel / Sucrose
Function / homology
Function and homology information


proboscis extension reflex / detection of chemical stimulus involved in sensory perception of taste / ionotropic sweet taste receptor activity / sweet taste receptor activity / taste receptor activity / sensory perception of sweet taste / ligand-gated monoatomic ion channel activity / sensory perception of taste / monoatomic ion transmembrane transport / signal transduction ...proboscis extension reflex / detection of chemical stimulus involved in sensory perception of taste / ionotropic sweet taste receptor activity / sweet taste receptor activity / taste receptor activity / sensory perception of sweet taste / ligand-gated monoatomic ion channel activity / sensory perception of taste / monoatomic ion transmembrane transport / signal transduction / membrane / plasma membrane
Similarity search - Function
Gustatory receptor / Trehalose receptor
Similarity search - Domain/homology
surcrose isoform / Gustatory receptor for sugar taste 64a
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsChen, Q.F. / Chen, R.Z. / Zhang, R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071202 China
National Natural Science Foundation of China (NSFC)32371261 China
CitationJournal: Cell Discov / Year: 2024
Title: Structure basis for sugar specificity of gustatory receptors in insects.
Authors: Ruizhu Chen / Ran Zhang / Lu Li / Bozhan Wang / Zhiwei Gao / Fenglian Liu / Yan Chen / Yutao Tian / Baobin Li / Qingfeng Chen /
History
DepositionMay 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gustatory receptor for sugar taste 64a
B: Gustatory receptor for sugar taste 64a
C: Gustatory receptor for sugar taste 64a
D: Gustatory receptor for sugar taste 64a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,6308
Polymers218,2604
Non-polymers1,3694
Water00
1


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

-
Components

#1: Protein
Gustatory receptor for sugar taste 64a


Mass: 54565.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: residues 465-472 correspond to the expression tag ,and residues 457-464 correspond to flexible linker.
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Gr64a, CG32261 / Production host: Homo sapiens (human) / References: UniProt: P83293
#2: Polysaccharide
alpha-D-glucopyranose-(1-2)-alpha-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: surcrose isoform
DescriptorTypeProgram
DGlcpa1-2DFrufaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2a_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Tetrameric sugar receptor Gr64a of Drosophila melanogaster (DmGr64a)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.052823 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F / Plasmid: PEZT-BM
Buffer solutionpH: 7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48.24 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 413565 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413204
ELECTRON MICROSCOPYf_angle_d0.76317908
ELECTRON MICROSCOPYf_dihedral_angle_d4.8311752
ELECTRON MICROSCOPYf_chiral_restr0.0462068
ELECTRON MICROSCOPYf_plane_restr0.0082184

+
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