[English] 日本語
Yorodumi
- EMDB-0979: Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0979
TitleRat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA and Calcium
Map datarefined map
Sample
  • Complex: GluD2
    • Protein or peptide: Glutamate receptor ionotropic, delta-2
Function / homology
Function and homology information


excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / ionotropic glutamate receptor complex / prepulse inhibition / regulation of neuron apoptotic process / glutamate-gated receptor activity / somatodendritic compartment / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / postsynaptic membrane / scaffold protein binding / dendritic spine / glutamatergic synapse / synapse / membrane / identical protein binding / 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, delta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsKumar J / Burada AP
Funding support India, 1 items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/5010023 India
CitationJournal: J Struct Biol / Year: 2020
Title: The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.
Authors: Ananth Prasad Burada / Rajesh Vinnakota / Janesh Kumar /
Abstract: GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple ...GluD2 receptor belongs to the orphan delta family of glutamate receptor ion channels. These receptors play key roles in synaptogenesis and synaptic plasticity and are associated with multiple neuronal disorders like schizophrenia, autism spectrum disorder, cerebellar ataxia, intellectual disability, paraplegia, retinal dystrophy, etc. Despite the importance of these receptors in CNS, insights into full-length GluD2 receptor structure is missing till-date. Here we report cryo-electron microscopy structure of the rat GluD2 receptor in the presence of calcium ions and the ligand 7-chlorokynurenic acid, elucidating its 3D architecture. The structure reveals a non-swapped architecture at the extracellular amino-terminal (ATD), and ligand-binding domain (LBD) interface similar to that observed in GluD1; however, the organization and arrangement of the ATD and LBD domains in GluD2 are unique. While our results demonstrate that non-swapped architecture is conserved in the delta receptor family, they also highlight the differences that exist between the two member receptors; GluD1 and GluD2.
History
DepositionJan 27, 2020-
Header (metadata) releaseJun 17, 2020-
Map releaseJun 17, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lu9
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lu9
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0979.png

Downloads & links

-
Map

FileDownload / File: emd_0979.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined map
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.316 / Movie #1: 0.4
Minimum - Maximum-0.46250916 - 0.95775163
Average (Standard dev.)0.0046592494 (±0.07678065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z392.000392.000392.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.4630.9580.005

-
Supplemental data

-
Mask #1

Fileemd_0979_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_0979_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_0979_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GluD2

EntireName: GluD2
Components
  • Complex: GluD2
    • Protein or peptide: Glutamate receptor ionotropic, delta-2

-
Supramolecule #1: GluD2

SupramoleculeName: GluD2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Recombinantly expressed protein
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI- / Recombinant plasmid: pEG Bac Mam
Molecular weightExperimental: 388 KDa

-
Macromolecule #1: Glutamate receptor ionotropic, delta-2

MacromoleculeName: Glutamate receptor ionotropic, delta-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 98.692242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DSIIHIGAIF DESAKKDDEV FRTAVGDLNQ NEEILQTEKI TFSVTFVDGN NPFQAVQEAC ELMNQGILAL VSSIGCTSAG SLQSLADAM HIPHLFIQRS TAGTPRSGCG LTRSNRNDDY TLSVRPPVYL NEVILRVVTE YAWQKFIIFY DSEYDIRGIQ E FLDKVSQQ ...String:
DSIIHIGAIF DESAKKDDEV FRTAVGDLNQ NEEILQTEKI TFSVTFVDGN NPFQAVQEAC ELMNQGILAL VSSIGCTSAG SLQSLADAM HIPHLFIQRS TAGTPRSGCG LTRSNRNDDY TLSVRPPVYL NEVILRVVTE YAWQKFIIFY DSEYDIRGIQ E FLDKVSQQ GMDVALQKVE NNINKMITTL FDTMRIEELN RYRDTLRRAI LVMNPATAKS FISEVVETNL VAFDCHWIII NE EINDVDV QELVRRSIGR LTIIRQTFPV PQNISQRCFR GNHRISSTLC DPKDPFAQNM EISNLYIYDT VLLLANAFHK KLQ DRKWHS MASLSCIRKN SKPWQGGRSM LETIKKGGVN GLTGDLEFGE NGGNPNVHFE ILGTNYGEEL GRGVRKLGCW NPVT GLNGS LTDKKLENNM RGVVLRVVTV LEEPFVMVSE NVLGKPKKYQ GFSIDVLDAL SNYLGFNYEI YVAPDHKYGS PQEDG TWNG LVGELVFKRA DIGISALTIT PDRENVVDFT TRYMDYSVGV LLRRAEKTVD MFACLAPFDL SLWACIAGTV LLVGLL VYL LNWLNPPRLQ MGSMTSTTLY NSMWFVYGSF VQQGGEVPYT TLATRMMMGA WWLFALIVIS SYTANLAAFL TITRIES SI QSLQDLSKQT DIPYGTVLDS AVYQHVRMKG LNPFERDSMY SQMWRMINRS NGSENNVLES QAGIQKVKYG NYAFVWDA A VLEYVAINDP DCSFYTVGNT VADRGYGIAL QHGSPYRDVF SQRILELQQS GDMDILKHKW WPKNGQCDLY SSVDAKQKG GALDIKSLAG VFCILAAGIV LSCLIAVLET WWSRRKGSRV PSKEDDKEID LEHLHRRVNS LCTDDDSPHK GLVPRGS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 8 / Details: 20mM Tris, 150mM NaCl, 0.75mM DDM, 0.025mM CHS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
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 / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Frames/image: 0-40 / Number real images: 4120 / Average exposure time: 6.0 sec. / Average electron dose: 40.38 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 61332 / Details: Particles were picked manually
CTF correctionSoftware - Name: Gctf (ver. v1.06) / Software - details: Gctf
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.13)
Final 3D classificationNumber classes: 2 / Avg.num./class: 5000 / Software - Name: cryoSPARC (ver. v2.13)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.13) / Software - details: local refinement
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.13) / Number images used: 7977

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6lu9:
Rat ionotropic Glutamate Delta-2 receptor in complex with 7-CKA and Calcium

+
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