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- EMDB-20717: GluA2 in complex with complex full-length in AS, bound to antagon... -

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Basic information

Entry
Database: EMDB / ID: EMD-20717
TitleGluA2 in complex with complex full-length in AS, bound to antagonist ZK200775
Map dataGluA2/CNIH3 complex full-length in AS, bound to antagonist ZK200775
Sample
  • Complex: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
    • Complex: Glutamate receptor 2
      • Protein or peptide: Glutamate receptor 2
    • Complex: Protein cornichon homolog 3
      • Protein or peptide: Protein cornichon homolog 3
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / localization within membrane / channel regulator activity / regulation of AMPA receptor activity / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head ...Cargo concentration in the ER / COPII-mediated vesicle transport / localization within membrane / channel regulator activity / regulation of AMPA receptor activity / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / neurotransmitter receptor localization to postsynaptic specialization membrane / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor clustering / cellular response to glycine / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / immunoglobulin binding / asymmetric synapse / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / conditioned place preference / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / vesicle-mediated transport / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated receptor activity / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / dendrite membrane / excitatory synapse / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / synaptic membrane / positive regulation of excitatory postsynaptic potential / dendritic shaft / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / regulation of membrane potential / protein tetramerization / establishment of protein localization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / postsynaptic density membrane / receptor internalization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / synaptic vesicle membrane / signaling receptor activity / amyloid-beta binding / presynapse / growth cone / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / 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 ...Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / 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 2 / Protein cornichon homolog 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsNakagawa T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human DevelopmentR01HD061543 United States
CitationJournal: Science / Year: 2019
Title: Structures of the AMPA receptor in complex with its auxiliary subunit cornichon.
Authors: Terunaga Nakagawa /
Abstract: In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes ...In the brain, AMPA-type glutamate receptors (AMPARs) form complexes with their auxiliary subunits and mediate the majority of fast excitatory neurotransmission. Signals transduced by these complexes are critical for synaptic plasticity, learning, and memory. The two major categories of AMPAR auxiliary subunits are transmembrane AMPAR regulatory proteins (TARPs) and cornichon homologs (CNIHs); these subunits share little homology and play distinct roles in controlling ion channel gating and trafficking of AMPAR. Here, I report high-resolution cryo-electron microscopy structures of AMPAR in complex with CNIH3. Contrary to its predicted membrane topology, CNIH3 lacks an extracellular domain and instead contains four membrane-spanning helices. The protein-protein interaction interface that dictates channel modulation and the lipids surrounding the complex are revealed. These structures provide insights into the molecular mechanism for ion channel modulation and assembly of AMPAR/CNIH3 complexes.
History
DepositionSep 13, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 18, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0522
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0522
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20717.png

Downloads & links

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Map

FileDownload / File: emd_20717.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluA2/CNIH3 complex full-length in AS, bound to antagonist ZK200775
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 180 pix.
= 383.76 Å		2.13 Å/pix.
x 180 pix.
= 383.76 Å		2.13 Å/pix.
x 180 pix.
= 383.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.132 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0522 / Movie #1: 0.0522
Minimum - Maximum-0.094162636 - 0.2102331
Average (Standard dev.)0.00017657797 (±0.0076787174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 383.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1322.1322.132
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z383.760383.760383.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0940.2100.000

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Supplemental data

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Sample components

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Entire : GluA2 in complex with CNIH3 full length at 4:4 stoichiometry

EntireName: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
Components
  • Complex: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
    • Complex: Glutamate receptor 2
      • Protein or peptide: Glutamate receptor 2
    • Complex: Protein cornichon homolog 3
      • Protein or peptide: Protein cornichon homolog 3

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Supramolecule #1: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry

SupramoleculeName: GluA2 in complex with CNIH3 full length at 4:4 stoichiometry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Bound to antagonist ZK200775 (MPQX). Lipid densities are observed.
Molecular weightTheoretical: 470 KDa

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Supramolecule #2: Glutamate receptor 2

SupramoleculeName: Glutamate receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK

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Supramolecule #3: Protein cornichon homolog 3

SupramoleculeName: Protein cornichon homolog 3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK

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Macromolecule #1: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE ...String:
MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KGYHYIIANL GFTDGDLLKI QFGGANVSGF QIVDYDDSLV SKFIERWSTL EEKEYPGAHT ATIKYTSALT YDAVQVMTEA FRNLRKQRIE ISRRGNAGDC LANPAVPWGQ GVEIERALKQ VQVEGLSGNI KFDQNGKRIN YTINIMELKT NGPRKIGYWS EVDKMVVTLT ELPSGNDTSG LENKTVVVTT ILESPYVMMK KNHEMLEGNE RYEGYCVDLA AEIAKHCGFK YKLTIVGDGK YGARDADTKI WNGMVGELVY GKADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY EWHTEEFEDG RETQSSESTN EFGIFNSLWF SLGAFMRQGC DISPRSLSGR IVGGVWWFFT LIIISSYTAN LAAFLTVERM VSPIESAEDL SKQTEIAYGT LDSGSTKEFF RRSKIAVFDK MWTYMRSAEP SVFVRTTAEG VARVRKSKGK YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SSLGNAVNLA VLKLNEQGLL DKLKNKWWYD KGECGSGGGD SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS QNSQNFATDY KDDDDKEGYN VYGIESVKI

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Macromolecule #2: Protein cornichon homolog 3

MacromoleculeName: Protein cornichon homolog 3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAFTFAAFCY MLSLVLCAAL IFFAIWHIIA FDELRTDFKS PIDQCNPVHA RERLRNIERI CFLLRKLVLP EYSIHSLFCI MFLCAQEWLT LGLNVPLLFY HFWRYFHCPA DSSELAYDPP VVMNADTLSY CQKEAWCKLA FYLLSFFYYL YCMIYTLVSS GGRGGTETSQ VAPA

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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
Component:
ConcentrationFormulaName
20.0 mMTrisHClTris
150.0 mMNaClsodium chloride
0.05 %GDNGDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11340 / Average exposure time: 6.0 sec. / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6780000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

2680

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.04) / Number images used: 218413
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.04)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.04)
Final 3D classificationNumber classes: 4 / Avg.num./class: 160000 / Software - Name: RELION (ver. 3.04)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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