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- EMDB-61751: Structure of glutamate receptor mGluD1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61751
TitleStructure of glutamate receptor mGluD1
Map data
Sample
  • Complex: Structure of ionotropic glutamate receptor mGluD1
    • 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: 3.9 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 glutamate receptor mGluD1
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_61751.png

Downloads & links

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Map

FileDownload / File: emd_61751.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å		0.86 Å/pix.
x 480 pix.
= 412.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.4669304 - 2.3467278
Average (Standard dev.)-0.00009368926 (±0.023726644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61751_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_61751_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 : Structure of ionotropic glutamate receptor mGluD1

EntireName: Structure of ionotropic glutamate receptor mGluD1
Components
  • Complex: Structure of ionotropic glutamate receptor mGluD1
    • Protein or peptide: Glutamate receptor ionotropic, delta-1

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Supramolecule #1: Structure of ionotropic glutamate receptor mGluD1

SupramoleculeName: Structure of ionotropic glutamate receptor mGluD1 / 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: 97.723438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEALTLWLLP WICQCVTVRA DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILA LVTSTGCASA NALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE L RWQKFVMF ...String:
MEALTLWLLP WICQCVTVRA DSIIHIGAIF EENAAKDDRV FQLAVSDLSL NDDILQSEKI TYSIKVIEAN NPFQAVQEAC DLMTQGILA LVTSTGCASA NALQSLTDAM HIPHLFVQRN PGGSPRTACH LNPSPDGEAY TLASRPPVRL NDVMLRLVTE L RWQKFVMF YDSEYDIRGL QSFLDQASRL GLDVSLQKVD KNISHVFTSL FTTMKTEELN RYRDTLRRAI LLLSPQGAHS FI NEAVETN LASKDSHWVF VNEEISDPEI LDLVHSALGR MTVVRQIFPS AKDNQKCMRN NHRISSLLCD PQEGYLQMLQ ISN LYLYDS VLMLANAFHR KLEDRKWHSM ASLNCIRKST KPWNGGRSML DTIKKGHITG LTGVMEFRED SSNPYVQFEI LGTT YSETF GKDMRKLATW DSEKGLNGSL QERPMGSRLQ GLTLKVVTVL EEPFVMVAEN ILGQPKRYKG FSIDVLDALA KALGF KYEI YQAPDGRYGH QLHNTSWNGM IGELISKRAD LAISAITITP ERESVVDFSK RYMDYSVGIL IKKPEEKISI FSLFAP FDF AVWACIAAAI PVVGVLIFVL NRIQAVRSQS ATQPRPSASA TLHSAIWIVY GAFVQQGGES SVNSVAMRIV MGSWWLF TL IVCSSYTANL AAFLTVSRMD NPIRTFQDLS KQLEMSYGTV RDSAVYEYFR AKGTNPLEQD STFAELWRTI SKNGGADN C VSNPSEGIRK AKKGNYAFLW DVAVVEYAAL TDDDCSVTVI GNSISSKGYG IALQHGSPYR DLFSQRILEL QDTGDLDVL KQKWWPHTGR CDLTSHSSTQ TEGKSLKLHS FAGVFCILAI GLLLACLVAA LELWWNSNRC HQETPKEDKE VN

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

Concentration6.3 mg/mL
BufferpH: 7.5
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: 936577
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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