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- EMDB-61757: Structure of ATD truncated glutamate receptor mGluD1 complexed wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-61757
TitleStructure of ATD truncated glutamate receptor mGluD1 complexed with GABA and Calcium
Map data
Sample
  • Complex: ATD truncated mGluD1 complexed with GABA and calcium
    • Protein or peptide: Glutamate receptor ionotropic, delta-1
Keywordsionotropic glutamate receptor / cation channel / complex / neurology / MEMBRANE PROTEIN
Function / homology
Function and homology information


GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels ...GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / postsynaptic membrane / glutamatergic synapse / metal ion binding / 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, delta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsDai Z / Yin YX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030081, 81874235 China
CitationJournal: To Be Published
Title: Structure of ATD truncated glutamate receptor mGluD1 complexed with GABA and Calcium
Authors: Dai Z / Yin YX
History
DepositionSep 29, 2024-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61757.png

Downloads & links

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Map

FileDownload / File: emd_61757.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.9028253 - 1.252375
Average (Standard dev.)-0.000101590325 (±0.022288362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 323.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61757_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61757_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATD truncated mGluD1 complexed with GABA and calcium

EntireName: ATD truncated mGluD1 complexed with GABA and calcium
Components
  • Complex: ATD truncated mGluD1 complexed with GABA and calcium
    • Protein or peptide: Glutamate receptor ionotropic, delta-1

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Supramolecule #1: ATD truncated mGluD1 complexed with GABA and calcium

SupramoleculeName: ATD truncated mGluD1 complexed with GABA and calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Glutamate receptor ionotropic, delta-1

MacromoleculeName: Glutamate receptor ionotropic, delta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.871832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSRLQGLTL KVVTVLEEPF VMVAENILGQ PKRYKGFSID VLDALAKALG FKYEIYQAPD GRYGHQLHNT SWNGMIGELI SKRADLAIS AITITPERES VVDFSKRYMD YSVGILIKKP EEKISIFSLF APFDFAVWAC IAAAIPVVGV LIFVLNRIQA V RSQSATQP ...String:
MGSRLQGLTL KVVTVLEEPF VMVAENILGQ PKRYKGFSID VLDALAKALG FKYEIYQAPD GRYGHQLHNT SWNGMIGELI SKRADLAIS AITITPERES VVDFSKRYMD YSVGILIKKP EEKISIFSLF APFDFAVWAC IAAAIPVVGV LIFVLNRIQA V RSQSATQP RPSASATLHS AIWIVYGAFV QQGGESSVNS VAMRIVMGSW WLFTLIVCSS YTANLAAFLT VSRMDNPIRT FQ DLSKQLE MSYGTVRDSA VYEYFRAKGT NPLEQDSTFA ELWRTISKNG GADNCVSNPS EGIRKAKKGN YAFLWDVAVV EYA ALTDDD CSVTVIGNSI SSKGYGIALQ HGSPYRDLFS QRILELQDTG DLDVLKQKWW PHTGRCDLTS HSSTQTEGKS LKLH SFAGV FCILAIGLLL ACLVAALELW WNSNRCHQET PKEDKEVNLE GGVEGGVEEN LYFQ

UniProtKB: Glutamate receptor ionotropic, delta-1

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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

Concentration6 mg/mL
BufferpH: 7.5
Details: 20mM HEPES pH 7.5, 150mM NaCl, 2mM CaCl2, 10mM GABA, 0.005% GDN
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 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: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1465382
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115655
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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