[English] 日本語
Yorodumi
- EMDB-9821: GluK3 receptor trapped in Desensitized state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9821
TitleGluK3 receptor trapped in Desensitized state
Map data
Sample
  • Complex: GluK3 complex with agonist SYM
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / monoatomic ion transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / perikaryon / chemical synaptic transmission / axon / dendrite / glutamatergic synapse / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsKumari J / Kumar J
Funding support India, 2 items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/501023 India
Department of Biotechnology (India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: Sci Rep / Year: 2019
Title: Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery.
Authors: Jyoti Kumari / Rajesh Vinnakota / Janesh Kumar /
Abstract: GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better ...GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.
History
DepositionFeb 13, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.863
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.863
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6jfy
  • Surface level: 0.863
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9821.png

Downloads & links

-
Map

FileDownload / File: emd_9821.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.863 / Movie #1: 0.863
Minimum - Maximum-2.0578704 - 3.3673804
Average (Standard dev.)0.0043503027 (±0.1422088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-2.0583.3670.004

-
Supplemental data

-
Half map: Half map A

Fileemd_9821_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_9821_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GluK3 complex with agonist SYM

EntireName: GluK3 complex with agonist SYM
Components
  • Complex: GluK3 complex with agonist SYM
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3

-
Supramolecule #1: GluK3 complex with agonist SYM

SupramoleculeName: GluK3 complex with agonist SYM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pEG BacMAM
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Glutamate receptor ionotropic, kainate 3

MacromoleculeName: Glutamate receptor ionotropic, kainate 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 91.305812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHVIRIGGI FEYADGPNAQ VMNAEEHAFR FSANIINRNR TLLPNTTLTY DIQRIHFHDS FEATKKACDQ LALGVVAIFG PSQGSTTNA VQSICNALEV PHIQLRWKHH PLDNKDTFYV NLYPDYASLS HAILDLVQSL KWRSATVVYD DSTGLIRLQE L IMAPSRYN ...String:
MPHVIRIGGI FEYADGPNAQ VMNAEEHAFR FSANIINRNR TLLPNTTLTY DIQRIHFHDS FEATKKACDQ LALGVVAIFG PSQGSTTNA VQSICNALEV PHIQLRWKHH PLDNKDTFYV NLYPDYASLS HAILDLVQSL KWRSATVVYD DSTGLIRLQE L IMAPSRYN IRLKIRQLPI DSDDSRPLLK EMKRGREFRI IFDCSHTMAA QILKQAMAMG MMTEYYHFIF TTLDLYALDL EP YRYSGVN LTGFRILNVD NPHVSAIVEK WSMERLQAAP RAESGLLDGV MMTDAALLYD AVHIVSVTYQ RAPQMTVNSL QCH RHKAWR FGGRFMNFIK EAQWEGLTGR IVFNKTSGLR TDFDLDIISL KEDGLEKVGV WSPADGLNIT EVAKGRGPNV TDSL TNRSL IVTTLLEEPF VMFRKSDRTL YGNDRFEGYC IDLLKELAHI LGFSYEIRLV EDGKYGAQDD KGQWNGMVKE LIDHK ADLA VAPLTITHVR EKAIDFSKPF MTLGVSILYR KPNGTNPSVF SFLNPLSPDI WMYVLLAYLG VSVVLFVIAR FSPYEW YDA HPCNPGSEVV ENNFTLLNSF WFGMGSLMQQ GSELMPKALS TRIIGGIWWF FTLIIISSYT ANLAAFLTVE RMESPID SA DDLAKQTKIE YGAVKDGATM TFFKKSKIST FEKMWAFMSS KPSALVKNNE EGIQRTLTAD YALLMESTTI EYITQRNC N LTQIGGLIDS KGYGIGTPMG SPYRDKITIA ILQLQEEDKL HIMKEKWWRG SGCPEEENKE ASALGIQKIG GIFIVLAAG LVLSVLVAV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.7 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClSodium chlorideSodium chloride
0.75 mMDDMDDM
0.03 mMCHScholesterol hemisuccinate
VitrificationCryogen name: ETHANE
DetailsPurified and detergent solubilized GluK3 receptors

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 719 / Average exposure time: 60.0 sec. / Average electron dose: 16.73 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware:
Namedetails
GctfgCTF was used for estimation
cryoSPARC (ver. 1)CTF correction
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3olz


Details: 3OLZ (ATD), XXXX(LBD), 5KUF(TM)
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC (ver. 1) / Software - details: Abinitio 3D reconstruction / Details: Abinitio 3D reconstruction module of cryosparc
Final 3D classificationNumber classes: 2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 1) / Software - details: cryoSPARC / Details: CryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Software - details: final reconstruction / Number images used: 9730

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6jfy:
GluK3 receptor trapped in Desensitized state

+
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