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- EMDB-52327: The NTD dimer and the interfacing LBD region of the AMPAR complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-52327
TitleThe NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state.
Map data
Sample
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsAMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / protein heterotetramerization / neuromuscular junction development / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / transmission of nerve impulse / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / membrane depolarization / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / glutamate-gated receptor activity / ionotropic glutamate receptor binding / presynaptic active zone membrane / somatodendritic compartment / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / calcium channel regulator activity / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / dendritic shaft / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / response to calcium ion / amyloid-beta binding / presynaptic membrane / protein homotetramerization / perikaryon / dendritic spine / postsynaptic membrane / postsynaptic density / neuronal cell body / dendrite / glutamatergic synapse / cell surface / protein-containing complex / membrane / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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 ...Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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 3 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus (rat) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPokharna A / Krieger J / Greger I / Ho H / Yamashita K / Cais O
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust223194/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
CitationJournal: To Be Published
Title: The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state.
Authors: Pokharna A / Krieger J / Greger I
History
DepositionDec 12, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52327.png

Downloads & links

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Map

FileDownload / File: emd_52327.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-43.356464000000003 - 66.79177
Average (Standard dev.)-0.000000000001227 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52327_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52327_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52327_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

EntireName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
Components
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

SupramoleculeName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus (rat)

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Macromolecule #1: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium ch...

MacromoleculeName: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 132.665734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV ...String:
GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV TARSVGNIKD VQEFRRIIEE MDRRQEKRYL IDCEVERINT ILEQVVILGK HSRGYHYMLA NLGFTDILLE RV MHGGANI TGFQIVNNEN PMVQQFIQRW VRLDEREFPE AKNAPLKYTS ALTHDAILVI AEAFRYLRRQ RVDVSRRGSA GDC LANPAV PWSQGIDIER ALKMVQVQGM TGNIQFDTYG RRTNYTIDVY EMKVSGSRKA GYWNEYERFV PFSDQQISND SSSS ENRTI VVTTILESPY VMYKKNHEQL EGNERYEGYC VDLAYEIAKH VGIKYKLSIV GDGKYGARDP ETKIWNGMVG ELVYG RADI AVAPLTITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVLFLVS RFSPYE WHL EDNNEEPRDP QSPPDPPNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTANLA AFLTVER MV SPIESAEDLA KQTEIAYGTL DSGSTKEFFR RSKIAVYEKM WSYMKSAEPS VFTKTTADGV ARVRKSKGKF AFLLESTM N EYIEQRKPCD TMKVGGNLDS KGYGVATPKG SALGTPVNLA VLKLSEQGIL DKLKNKWWYD KGECGAKDSG SKDKTSALS LSNVAGVFYI LVGGLGLAMM VALIEFCYKS RAESKRMKLT KNTQNFKPAP AGGSGSGGLF DRGVQMLLTT VGAFAAFSLM TIAVGTDYW LYSRGVCKTK SVSENETSKK NEEVMTHSGL WRTCCLEGNF KGLCKQIDHF PEDADYEADT AEYFLRAVRA S SIFPILSV ILLFMGGLCI AASEFYKTRH NIILSAGIFF VSAGLSNIIG IIVYISANAG DPSKSDSKKN SYSYGWSFYF GA LSFIIAE MVGVLAVHMF IDRHKQLRAT ARATDYLQAS AITRIPSYRY RYQRRSRSSS RSTEPSHSRD ASPVGVKGFN TLP STEISM YTLSRDPLKA ATTPTATYNS DRDNSFLQVH NCIQKDSKDS LHANTANRRT TPV

UniProtKB: Glutamate receptor 3, Voltage-dependent calcium channel gamma-2 subunit

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 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: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 264366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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