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- EMDB-49889: Human delta 2 receptor activated by D-serine -

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Basic information

Entry
Database: EMDB / ID: EMD-49889
TitleHuman delta 2 receptor activated by D-serine
Map dataFull map locally sharpened
Sample
  • Complex: Human delta-2 receptor
    • Protein or peptide: Glutamate receptor ionotropic, delta-2
  • Ligand: D-SERINE
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: 3.69 Å
AuthorsWang H / 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_49889.png

Downloads & links

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Map

FileDownload / File: emd_49889.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map locally sharpened
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 420 pix.
= 407.4 Å		0.97 Å/pix.
x 420 pix.
= 407.4 Å		0.97 Å/pix.
x 420 pix.
= 407.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.29866534 - 0.43664792
Average (Standard dev.)0.00044664598 (±0.005387475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 407.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: ECD map locally sharpened

Fileemd_49889_additional_1.map
AnnotationECD map locally sharpened
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Additional map: ECD map half a

Fileemd_49889_additional_2.map
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Additional map: ECD map half b

Fileemd_49889_additional_3.map
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Additional map: TMD map locally sharpened

Fileemd_49889_additional_4.map
AnnotationTMD map locally sharpened
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Additional map: TMD map half a

Fileemd_49889_additional_5.map
AnnotationTMD map half a
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Additional map: TMD map half b

Fileemd_49889_additional_6.map
AnnotationTMD map half b
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Half map: Full map half b

Fileemd_49889_half_map_1.map
AnnotationFull map half b
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Half map: Full map half a

Fileemd_49889_half_map_2.map
AnnotationFull map half a
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Sample components

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Entire : Human delta-2 receptor

EntireName: Human delta-2 receptor
Components
  • Complex: Human delta-2 receptor
    • Protein or peptide: Glutamate receptor ionotropic, delta-2
  • Ligand: D-SERINE

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Supramolecule #1: Human delta-2 receptor

SupramoleculeName: Human delta-2 receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 94.287391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IHIGAIFDES AKKDDEVFRT AVGDLNQNEE ILQTEKITFS VTFVDGNNPF QAVQEACELM NQGILALVSS IGCTSAGSLQ SLADAMHIP HLFIQRSTAG TPRSGCGLTR SNRNDDYTLS VRPPVYLHDV ILRVVTEYAW QKFIIFYDSE YDIRGIQEFL D KVSQQGMD ...String:
IHIGAIFDES AKKDDEVFRT AVGDLNQNEE ILQTEKITFS VTFVDGNNPF QAVQEACELM NQGILALVSS IGCTSAGSLQ SLADAMHIP HLFIQRSTAG TPRSGCGLTR SNRNDDYTLS VRPPVYLHDV ILRVVTEYAW QKFIIFYDSE YDIRGIQEFL D KVSQQGMD VALQKVENNI NKMITTLFDT MRIEELNRYR DTLRRAILVM NPATAKSFIT EVVETNLVAF DCHWIIINEE IN DVDVQEL VRRSIGRLTI IRQTFPVPQN ISQRCFRGNH RISSTLCDPK DPFAQNMEIS NLYIYDTVLL LANAFHKKLE DRK WHSMAS LSCIRKNSKP WQGGRSMLET IKKGGVSGLT GELEFGENGG NPNVHFEILG TNYGEELGRG VRKLGCWNPV TGLN GSLTD KKLENNMRGV VLRVVTVLEE PFVMVSENVL GKPKKYQGFS IDVLDALSNY LGFNYEIYVA PDHKYGSPQE DGTWN GLVG ELVFKRADIG ISALTITPDR ENVVDFTTRY MDYSVGVLLR RAEKTVDMFA CLAPFDLSLW ACIAGTVLLV GLLVYL LNW LNPPRLQMGS MTSTTLYNSM WFVYGSFVQQ GGEVPYTTLA TRMMMGAWWL FALIVISSYT ANLAAFLTIT RIESSIQ SL QDLSKQTEIP YGTVLDSAVY EHVRMKGLNP FERDSMYSQM WRMINRSNGS ENNVLESQAG IQKVKYGNYA FVWDAAVL E YVAINDPDCS FYTIGNTVAD RGYGIALQHG SPYRDVFSQR ILELQQNGDM DILKHKWWPK NGQCDLYSSV DTKQKGGAL DIKSFAGVFC ILAAGIVLSC FIAMLETWWN KRKGSR

UniProtKB: Glutamate receptor ionotropic, delta-2

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Macromolecule #2: D-SERINE

MacromoleculeName: D-SERINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: DSN
Molecular weightTheoretical: 105.093 Da
Chemical component information

ChemComp-DSN:
D-SERINE

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69080
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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