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- EMDB-43242: Transmembrane AMPA Receptor Regulatory Protein Subunit Gamma 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-43242
TitleTransmembrane AMPA Receptor Regulatory Protein Subunit Gamma 2
Map datalocally filtered map
Sample
  • Complex: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
Keywordstetraspanin / glutamate receptor regulator protein / Claudin-like / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process ...Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / transmission of nerve impulse / AMPA glutamate receptor complex / membrane depolarization / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / ionotropic glutamate receptor binding / somatodendritic compartment / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / postsynaptic density membrane / Schaffer collateral - CA1 synapse / response to calcium ion / glutamatergic synapse / cell surface
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
Similarity search - Domain/homology
Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsHale WD / Montano Romero A / Huganir RL / Twomey EC
Funding support United States, 5 items
OrganizationGrant numberCountry
Other privateKinship Foundation 22098168
Other privateDiana Helis Henry Medical Research Foundation 142548
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH112152 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS036715 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH132811 United States
CitationJournal: bioRxiv / Year: 2023
Title: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit γ2.
Authors: W Dylan Hale / Alejandra Montaño Romero / Richard L Huganir / Edward C Twomey /
Abstract: Transmembrane AMPA receptor regulatory proteins (TARPs) are claudin-like proteins that tightly regulate AMPA receptors (AMPARs) and are fundamental for excitatory neurotransmission. We used cryo- ...Transmembrane AMPA receptor regulatory proteins (TARPs) are claudin-like proteins that tightly regulate AMPA receptors (AMPARs) and are fundamental for excitatory neurotransmission. We used cryo-electron microscopy (cryo-EM) to reconstruct the 36 kDa TARP subunit γ2 to 2.3 Å and reveal the structural diversity of TARPs. Our data reveals critical motifs that distinguish TARPs from claudins and define how sequence variations within TARPs differentiate subfamilies and their regulation of AMPARs.
History
DepositionJan 2, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43242.png

Downloads & links

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Map

FileDownload / File: emd_43242.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocally filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.583156 - 7.299593
Average (Standard dev.)0.000063372354 (±0.017049184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A

Fileemd_43242_half_map_1.map
AnnotationHalf A
Projections & Slices
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Histogram

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Half map: Half B

Fileemd_43242_half_map_2.map
AnnotationHalf B
Projections & Slices
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Sample components

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Entire : Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2

EntireName: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2
Components
  • Complex: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit

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Supramolecule #1: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2

SupramoleculeName: Structure of Transmembrane AMPA Receptor Regulatory Protein Subunit g2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Strain: Expi293 Gnti-

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Macromolecule #1: Voltage-dependent calcium channel gamma-2 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.196709 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD ...String:
MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD SKKNSYSYGW SFYFGALSFI IAEMVGVLAV HMFIDRHKQL TG

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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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 / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Generated ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 494916
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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