[English] 日本語
Yorodumi
- EMDB-32032: GluK3 D759G mutant receptor complex with UBP310 and spermine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32032
TitleGluK3 D759G mutant receptor complex with UBP310 and spermine
Map dataGluK3D759G mutant in complex with UBP310 and spermine
Sample
  • Complex: GluK3 D759G mutant receptor complex with UBP310 and spermine
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / 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 ...Presynaptic function of Kainate receptors / 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 / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / 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: 5.9 Å
AuthorsAssaiya A / Kumar J
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2020/003971 India
CitationJournal: To Be Published
Title: GluK3 D759G mutant receptor in complex with UBP310 and Spermine
Authors: Assaiya A / Kumar J
History
DepositionOct 6, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32032.png

Downloads & links

-
Map

FileDownload / File: emd_32032.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK3D759G mutant in complex with UBP310 and spermine
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.7315164 - 2.1023765
Average (Standard dev.)0.0028602823 (±0.064353056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 420.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : GluK3 D759G mutant receptor complex with UBP310 and spermine

EntireName: GluK3 D759G mutant receptor complex with UBP310 and spermine
Components
  • Complex: GluK3 D759G mutant receptor complex with UBP310 and spermine
    • Protein or peptide: Glutamate receptor ionotropic, kainate 3

-
Supramolecule #1: GluK3 D759G mutant receptor complex with UBP310 and spermine

SupramoleculeName: GluK3 D759G mutant receptor complex with UBP310 and spermine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pEGBacMam
Molecular weightTheoretical: 364 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: 91.247781 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 ILQLQEEGKL HIMKEKWWRG SGCPEEENKE ASALGIQKIG GIFIVLAAG LVLSVLVAV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 43.72 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jfz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7vm2:
GluK3 D759G mutant receptor complex with UBP310 and spermine

+
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://pdbjlvh1.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