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- EMDB-32032: GluK3 D759G mutant receptor complex with UBP310 and spermine -

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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
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / 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 / postsynaptic membrane / axon / dendrite / glutamatergic synapse / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32032.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420.8 Å		1.05 Å/pix.
x 400 pix.
= 420.8 Å		1.05 Å/pix.
x 400 pix.
= 420.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
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 °

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Supplemental data

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Sample components

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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

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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)
Molecular weightTheoretical: 364 KDa

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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

UniProtKB: Glutamate receptor ionotropic, kainate 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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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

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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