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- EMDB-49890: Human delta 2 receptor in the resting state with ATD deleted -

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Basic information

Entry
Database: EMDB / ID: EMD-49890
TitleHuman delta 2 receptor in the resting state with ATD deleted
Map dataWhole map locally sharpened
Sample
  • Complex: Tetrameric human delta-2 receptor with ATD deleted
    • Protein or peptide: Glutamate receptor ionotropic, delta-2
Keywordsligand-gated ion channel / ion channel / neurotransmitter receptor / TRANSPORT PROTEIN
Function / homology
Function and homology information


trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / heterophilic cell-cell adhesion / glutamate receptor signaling pathway ...trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / heterophilic cell-cell adhesion / glutamate receptor signaling pathway / parallel fiber to Purkinje cell synapse / regulation of neuron projection development / AMPA glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / regulation of presynapse assembly / prepulse inhibition / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of neuron apoptotic process / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular protein localization / scaffold protein binding / dendritic spine / synapse / 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 / 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 ionotropic, delta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsWang W / Ahmed F / Kumar Mondal A / Twomey EC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154904 United States
CitationJournal: Nature / Year: 2025
Title: Delta-type glutamate receptors are ligand-gated ion channels.
Authors: Haobo Wang / Fairine Ahmed / Jeffrey Khau / Anish Kumar Mondal / Edward C Twomey /
Abstract: Delta-type ionotropic glutamate receptors (iGluRs, also known as GluDs) are members of the iGluR ligand-gated ion channel family, yet their function remains unknown. Although GluDs are widely ...Delta-type ionotropic glutamate receptors (iGluRs, also known as GluDs) are members of the iGluR ligand-gated ion channel family, yet their function remains unknown. Although GluDs are widely expressed in the brain, have key roles in synaptic organization, and harbour disease-linked mutations, whether they retain iGluR-like channel function is debated as currents have not been directly observed. Here we define GluDs as ligand-gated ion channels that are tightly regulated in cellular contexts by purifying human GluD2 (hGluD2) and directly characterizing its structure and function using cryo-electron microscopy and bilayer recordings. We show that hGluD2 is activated by D-serine and GABA (γ-aminobutyric acid), with augmented activation at physiological temperatures. We reveal that hGluD2 contains an ion channel directly coupled to clamshell-like ligand-binding domains, which are coordinated by the amino-terminal domain above the ion channel. Ligand binding triggers channel opening via an asymmetric mechanism, and a cerebellar ataxia point mutation in the ligand-binding domain rearranges the receptor architecture and induces leak currents. Our findings demonstrate that GluDs possess the intrinsic biophysical properties of ligand-gated ion channels, reconciling prior conflicting observations to establish a framework for understanding their cellular regulation and for developing therapies targeting GluD2.
History
DepositionMar 24, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49890.png

Downloads & links

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Map

FileDownload / File: emd_49890.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWhole map locally sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.2831156 - 3.1150718
Average (Standard dev.)0.0014135201 (±0.030943679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: TMD map locally sharpened

Fileemd_49890_additional_1.map
AnnotationTMD map locally sharpened
Projections & Slices
AxesZYX

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Additional map: TMD map half a

Fileemd_49890_additional_2.map
AnnotationTMD map half a
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Additional map: LBD map half a

Fileemd_49890_additional_3.map
AnnotationLBD map half a
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Additional map: LBD map half b

Fileemd_49890_additional_4.map
AnnotationLBD map half b
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Additional map: LBD map locally sharpened

Fileemd_49890_additional_5.map
AnnotationLBD map locally sharpened
Projections & Slices
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Histogram

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Additional map: TMD map half b

Fileemd_49890_additional_6.map
AnnotationTMD map half b
Projections & Slices
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Half map: Whole map half b

Fileemd_49890_half_map_1.map
AnnotationWhole map half b
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Whole map half a

Fileemd_49890_half_map_2.map
AnnotationWhole map half a
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Sample components

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Entire : Tetrameric human delta-2 receptor with ATD deleted

EntireName: Tetrameric human delta-2 receptor with ATD deleted
Components
  • Complex: Tetrameric human delta-2 receptor with ATD deleted
    • Protein or peptide: Glutamate receptor ionotropic, delta-2

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Supramolecule #1: Tetrameric human delta-2 receptor with ATD deleted

SupramoleculeName: Tetrameric human delta-2 receptor with ATD deleted / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutamate receptor ionotropic, delta-2

MacromoleculeName: Glutamate receptor ionotropic, delta-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.553383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VVLRVVTVLE EPFVMVSENV LGKPKKYQGF SIDVLDALSN YLGFNYEIYV APDHKYGSPQ EDGTWNGLVG ELVFKRADIG ISALTITPD RENVVDFTTR YMDYSVGVLL RRAEKTVDMF ACLAPFDLSL WACIAGTVLL VGLLVYLLNW LNPPRLQMGS M TSTTLYNS ...String:
VVLRVVTVLE EPFVMVSENV LGKPKKYQGF SIDVLDALSN YLGFNYEIYV APDHKYGSPQ EDGTWNGLVG ELVFKRADIG ISALTITPD RENVVDFTTR YMDYSVGVLL RRAEKTVDMF ACLAPFDLSL WACIAGTVLL VGLLVYLLNW LNPPRLQMGS M TSTTLYNS MWFVYGSFVQ QGGEVPYTTL ATRMMMGAWW LFALIVISSY TANLAAFLTI TRIESSIQSL QDLSKQTEIP YG TVLDSAV YEHVRMKGLN PFERDSMYSQ MWRMINRSNG SENNVLESQA GIQKVKYGNY AFVWDAAVLE YVAINDPDCS FYT IGNTVA DRGYGIALQH GSPYRDVFSQ RILELQQNGD MDILKHKWWP KNGQCDLYSS VDTKQKGGAL DIKSFAGVFC ILAA GIVLS CFIAMLETWW NKRKGSR

UniProtKB: Glutamate receptor ionotropic, delta-2

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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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114411
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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