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- EMDB-66179: GRM1-Acc State Conformation 2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66179
TitleGRM1-Acc State Conformation 2
Map datacomposite map
Sample
  • Complex: GRM1
    • Protein or peptide: Metabotropic glutamate receptor 1
  • Ligand: GAMMA-L-GLUTAMIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL
  • Ligand: N-[4-(trifluoromethyl)-1,3-oxazol-2-yl]-9H-xanthene-9-carboxamide
KeywordsReceptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


dendriole / : / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / : / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / cellular response to electrical stimulus / synaptic signaling via neuropeptide / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway ...dendriole / : / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / : / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / cellular response to electrical stimulus / synaptic signaling via neuropeptide / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of sensory perception of pain / L-glutamate import across plasma membrane / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / regulation of synaptic transmission, glutamatergic / sensory perception of pain / locomotory behavior / postsynaptic density membrane / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / Sensory perception of sweet, bitter, and umami (glutamate) taste / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain ...GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLu Y / Wen TL / Shen YQ / Yang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: GRM1-Acc State Conformation 2
Authors: Lu Y / Wen TL / Shen YQ / Yang X
History
DepositionSep 11, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66179.png

Downloads & links

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Map

FileDownload / File: emd_66179.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å

Surface

Projections

Slices (1/3)

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: 0.006
Minimum - Maximum-0.010953939 - 0.071019135
Average (Standard dev.)0.000056173103 (±0.0010677704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GRM1

EntireName: GRM1
Components
  • Complex: GRM1
    • Protein or peptide: Metabotropic glutamate receptor 1
  • Ligand: GAMMA-L-GLUTAMIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHLORIDE ION
  • Ligand: CHOLESTEROL
  • Ligand: N-[4-(trifluoromethyl)-1,3-oxazol-2-yl]-9H-xanthene-9-carboxamide

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Supramolecule #1: GRM1

SupramoleculeName: GRM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Metabotropic glutamate receptor 1

MacromoleculeName: Metabotropic glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.322344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKTG ASSQRSVARM DGDVIIGALF SVHHQPPAEK VPERKCGEIR EQYGIQRVEA MFHTLDKINA DPVLLPNITL GSEIRDSCW HSSVALEQSI EFIRDSLISI RDEKDGINRC LPDGQSLPPG RTKKPIAGVI GPGSSSVAIQ VQNLLQLFDI P QIAYSATS ...String:
DYKDDDDKTG ASSQRSVARM DGDVIIGALF SVHHQPPAEK VPERKCGEIR EQYGIQRVEA MFHTLDKINA DPVLLPNITL GSEIRDSCW HSSVALEQSI EFIRDSLISI RDEKDGINRC LPDGQSLPPG RTKKPIAGVI GPGSSSVAIQ VQNLLQLFDI P QIAYSATS IDLSDKTLYK YFLRVVPSDT LQARAMLDIV KRYNWTYVSA VHTEGNYGES GMDAFKELAA QEGLCIAHSD KI YSNAGEK SFDRLLRKLR ERLPKARVVV CFCEGMTVRG LLSAMRRLGV VGEFSLIGSD GWADRDEVIE GYEVEANGGI TIK LQSPEV RSFDDYFLKL RLDTNTRNPW FPEFWQHRFQ CRLPGHLLEN PNFKRICTGN ESLEENYVQD SKMGFVINAI YAMA HGLQN MHHALCPGHV GLCDAMKPID GSKLLDFLIK SSFIGVSGEE VWFDEKGDAP GRYDIMNLQY TEANRYDYVH VGTWH EGVL NIDDYKIQMN KSGVVRSVCS EPCLKGQIKV IRKGEVSCCW ICTACKENEY VQDEFTCKAC DLGWWPNADL TGCEPI PVR YLEWSNIESI IAIAFSCLGI LVTLFVTLIF VLYRDTPVVK SSSRELCYII LAGIFLGYVC PFTLIAKPTT TSCYLQR LL VGLSSAMCYS ALVTKTNRIA RILAGSKKKI CTRKPRFMSA WAQVIIASIL ISVQLTLVVT LIIMEPPMPI LSYPSIKE V YLICNTSNLG VVAPLGYNGL LIMSCTYYAF KTRNVPANFN EAKYIAFTMY TTCIIWLAFV PIYFGSNYKI ITTCFAVSL SVTVALGCMF TPKMYIIIAK PERNVRSAFT TSDVVRMHVG DGKLPCRSNT FLNIFRRKKA GAGNANSNG

UniProtKB: Metabotropic glutamate receptor 1

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Macromolecule #2: GAMMA-L-GLUTAMIC ACID

MacromoleculeName: GAMMA-L-GLUTAMIC ACID / type: ligand / ID: 2 / Number of copies: 2 / Formula: GGL
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GGL:
GAMMA-L-GLUTAMIC ACID

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: N-[4-(trifluoromethyl)-1,3-oxazol-2-yl]-9H-xanthene-9-carboxamide

MacromoleculeName: N-[4-(trifluoromethyl)-1,3-oxazol-2-yl]-9H-xanthene-9-carboxamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1EX5
Molecular weightTheoretical: 360.287 Da

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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: 7.2
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 19.0 µm / Nominal defocus min: 6.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE / Details: CryoSPARC Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 59726
Initial angle assignmentType: OTHER
Final angle assignmentType: ANGULAR RECONSTITUTION

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