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- EMDB-23542: Structure of full-length GluK1 with L-Glu -

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Basic information

Entry
Database: EMDB / ID: EMD-23542
TitleStructure of full-length GluK1 with L-Glu
Map dataGluK1 with L-Glu (full-length
Sample
  • Complex: GluK1 tetrameric complex
    • Protein or peptide: Isoform Glur5-2 of Glutamate receptor ionotropic, kainate 1
Function / homology
Function and homology information


: / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...: / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / glutamate binding / adult behavior / behavioral response to pain / membrane depolarization / kainate selective glutamate receptor activity / ligand-gated monoatomic ion channel activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / excitatory postsynaptic potential / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / positive regulation of synaptic transmission, GABAergic / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / signaling receptor activity / presynaptic membrane / nervous system development / chemical synaptic transmission / postsynaptic membrane / postsynaptic density / receptor complex / neuronal cell body / dendrite / synapse / glutamatergic 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, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsMeyerson JR / Selvakumar P
CitationJournal: Cell Rep / Year: 2021
Title: Structural and compositional diversity in the kainate receptor family.
Authors: Purushotham Selvakumar / Joon Lee / Nandish Khanra / Changhao He / Hermany Munguba / Lisa Kiese / Johannes Broichhagen / Andreas Reiner / Joshua Levitz / Joel R Meyerson /
Abstract: The kainate receptors (KARs) are members of the ionotropic glutamate receptor family and assemble into tetramers from a pool of five subunit types (GluK1-5). Each subunit confers distinct functional ...The kainate receptors (KARs) are members of the ionotropic glutamate receptor family and assemble into tetramers from a pool of five subunit types (GluK1-5). Each subunit confers distinct functional properties to a receptor, but the compositional and stoichiometric diversity of KAR tetramers is not well understood. To address this, we first solve the structure of the GluK1 homomer, which enables a systematic assessment of structural compatibility among KAR subunits. Next, we analyze single-cell RNA sequencing data, which reveal extreme diversity in the combinations of two or more KAR subunits co-expressed within the same cell. We then investigate the composition of individual receptor complexes using single-molecule fluorescence techniques and find that di-heteromers assembled from GluK1, GluK2, or GluK3 can form with all possible stoichiometries, while GluK1/K5, GluK2/K5, and GluK3/K5 can form 3:1 or 2:2 complexes. Finally, using three-color single-molecule imaging, we discover that KARs can form tri- and tetra-heteromers.
History
DepositionFeb 26, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 10, 2021-
Current statusNov 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.366
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.366
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lvt
  • Surface level: 0.366
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lvt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23542.png

Downloads & links

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Map

FileDownload / File: emd_23542.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluK1 with L-Glu (full-length
Voxel sizeX=Y=Z: 1.096 Å
Density
Contour LevelBy AUTHOR: 0.366 / Movie #1: 0.366
Minimum - Maximum-0.9868582 - 1.872258
Average (Standard dev.)0.0015781845 (±0.063096225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 350.71997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.9871.8720.002

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Supplemental data

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Additional map: GluK1 with L-Glu (ATD)

Fileemd_23542_additional_1.map
AnnotationGluK1 with L-Glu (ATD)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: GluK1 with L-Glu (LBD-TMD)

Fileemd_23542_additional_2.map
AnnotationGluK1 with L-Glu (LBD-TMD)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GluK1 tetrameric complex

EntireName: GluK1 tetrameric complex
Components
  • Complex: GluK1 tetrameric complex
    • Protein or peptide: Isoform Glur5-2 of Glutamate receptor ionotropic, kainate 1

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Supramolecule #1: GluK1 tetrameric complex

SupramoleculeName: GluK1 tetrameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Isoform Glur5-2 of Glutamate receptor ionotropic, kainate 1

MacromoleculeName: Isoform Glur5-2 of Glutamate receptor ionotropic, kainate 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 102.562078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRIGG IFETVENEPV NVEELAFKFA VTSINRNRTL MPNTTLTYDI QRINLFDSF EASRRACDQL ALGVAALFGP SHSSSVSAVQ SICNALEVPH IQTRWKHPSV DSRDLFYINL YPDYAAISRA V LDLVLYYN ...String:
MKIISPVLSN LVFSRSIKVL LCLLWIGYSQ GTTHVLRIGG IFETVENEPV NVEELAFKFA VTSINRNRTL MPNTTLTYDI QRINLFDSF EASRRACDQL ALGVAALFGP SHSSSVSAVQ SICNALEVPH IQTRWKHPSV DSRDLFYINL YPDYAAISRA V LDLVLYYN WKTVTVVYED STGLIRLQEL IKAPSRYNIK IKIRQLPPAN KDAKPLLKEM KKSKEFYVIF DCSHETAAEI LK QILFMGM MTEYYHYFFT TLDLFALDLE LYRYSGVNMT GFRLLNIDNP HVSSIIEKWS MERLQAPPRP ETGLLDGMMT TEA ALMYDA VYMVAIASHR ASQLTVSSLQ CHRHKPWRLG PRFMNLIKEA RWDGLTGRIT FNKTDGLRKD FDLDIISLKE EGTE KIGIW NSNSGLNMTD GNRDRSNNIT DSLANRTLIV TTILEEPYVM YRKSDKPLYG NDRFEGYCLD LLKELSNILG FLYDV KLVP DGKYGAQNDK GEWNGMVKEL IDHRADLAVA PLTITYVREK VIDFSKPFMT LGISILYRKP NGTNPGVFSF LNPLSP DIW MYVLLACLGV SCVLFVIARF TPYEWYNPHP CNPDSDVVEN NFTLLNSFWF GVGALMQQGS ELMPKALSTR IVGGIWW FF TLIIISSYTA NLAAFLTVER MESPIDSADD LAKQTKIEYG AVRDGSTMTF FKKSKISTYE KMWAFMSSRQ QSALVKNS D EGIQRVLTTD YALLMESTSI EYVTQRNCNL TQIGGLIDSK GYGVGTPIGS PYRDKITIAI LQLQEEGKLH MMKEKWWRG NGCPEEDSKE ASALGVENIG GIFIVLAAGL VLSVFVAIGE FLYKSRKNND VEQCLSFNAI MEELGISLKN QKKLKKKSRT KGKSSFTSI LTCHQRRTQR KETVA

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 321611
FSC plot (resolution estimation)

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