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- EMDB-70615: mGluR7 in native membrane vesicles -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70615
TitlemGluR7 in native membrane vesicles
Map datamGluR7 in reconstituted vesicles
Sample
  • Complex: mGLuR7
    • Protein or peptide: Metabotropic glutamate receptor 7
KeywordsGPCR / Class C / membrane protein / cluster
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / negative regulation of glutamate secretion / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / glutamate binding ...group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / negative regulation of glutamate secretion / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / glutamate binding / axon development / presynaptic active zone / asymmetric synapse / regulation of synaptic transmission, glutamatergic / dendritic shaft / PDZ domain binding / sensory perception of sound / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell cortex / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / receptor complex / protein dimerization activity / axon / calcium ion binding / dendrite / membrane / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 7 / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site ...GPCR, family 3, metabotropic glutamate receptor 7 / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / 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 / G-protein coupled receptors family 3 signature 3. / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMandala V / Fu Z / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular contacts in self-assembling clusters of membrane proteins.
Authors: Venkata Shiva Mandala / Ziao Fu / Roderick MacKinnon /
Abstract: Motivated by recent data pointing to the existence of homo-oligomeric assemblies of membrane proteins called higher-order transient structures, and their apparent role in connecting components of ...Motivated by recent data pointing to the existence of homo-oligomeric assemblies of membrane proteins called higher-order transient structures, and their apparent role in connecting components of membrane signal pathways, we examine here by cryoelectron microscopy some of the protein-protein interactions that occur in cluster formation. Metabotropic glutamate receptors and HCN ion channels inside clusters contact their neighbors through structured extracellular and intracellular domains, respectively. Other ion channels, including Kv2.1 and Slo1, appear to form clusters through prominent intrinsically disordered sequences in the cytoplasm. These distinct modes of interaction are associated with clusters exhibiting varying degrees of compactness and order. We conclude that nature utilizes a variety of ways to form connections between membrane proteins in self-assembled clusters.
History
DepositionMay 14, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70615.png

Downloads & links

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Map

FileDownload / File: emd_70615.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationmGluR7 in reconstituted vesicles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 180 pix.
= 267.48 Å		1.49 Å/pix.
x 180 pix.
= 267.48 Å		1.49 Å/pix.
x 180 pix.
= 267.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.486 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0838
Minimum - Maximum-1.3915235 - 2.283147
Average (Standard dev.)0.0017513662 (±0.03383106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 267.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfA

Fileemd_70615_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_70615_half_map_2.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mGLuR7

EntireName: mGLuR7
Components
  • Complex: mGLuR7
    • Protein or peptide: Metabotropic glutamate receptor 7

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Supramolecule #1: mGLuR7

SupramoleculeName: mGLuR7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Metabotropic glutamate receptor 7

MacromoleculeName: Metabotropic glutamate receptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.834938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFAGGGG SPSRLEEELR RRLTEPQEMY APHSIRIEGD VTLGGLFPVH AKGPSGVPCG DIKRENGIHR LEAMLYALD QINSDPNLLP NVTLGARILD TCSRDTYALE QSLTFVQALI QKDTSDVRCT NGEPPVFVKP EKVVGVIGAS G SSVSIMVA ...String:
MKTIIALSYI FCLVFAGGGG SPSRLEEELR RRLTEPQEMY APHSIRIEGD VTLGGLFPVH AKGPSGVPCG DIKRENGIHR LEAMLYALD QINSDPNLLP NVTLGARILD TCSRDTYALE QSLTFVQALI QKDTSDVRCT NGEPPVFVKP EKVVGVIGAS G SSVSIMVA NILRLFQIPQ ISYASTAPEL SDDRRYDFFS RVVPPDSFQA QAMVDIVKAL GWNYVSTLAS EGSYGEKGVE SF TQISKEA GGLCIAQSVR IPQERKDRTI DFDRIIKQLL DTPNSRAVVI FANDEDIKQI LAAAKRADQV GHFLWVGSDS WGS KINPLH QHEDIAEGAI TIQPKRATVE GFDAYFTSRT LENNRRNVWF AEYWEENFNC KLTISGSKKE DTDRKCTGQE RIGK DSNYE QEGKVQFVID AVYAMAHALH HMNKDLCADY RGVCPEMEQA GGKKLLKYIR NVNFNGSAGT PVMFNKNGDA PGRYD IFQY QTTNTSNPGY RLIGQWTDEL QLNIEDMQWG KGVREIPASV CTLPCKPGQR KKTQKGTPCC WTCEPCDGYQ YQFDEM TCQ HCPYDQRPNE NRTGCQDIPI IKLEWHSPWA VIPVFLAMLG IIATIFVMAT FIRYNDTPIV RASGRELSYV LLTGIFL CY IITFLMIAKP DVAVCSFRRV FLGLGMCISY AALLTKTYRI YRIFEQGKKS VTAPRLISPT SQLAITSSLI SVQLLGVF I WFIVDPPNII IDYDEHKTMN PEQARGVLKC DITDLQIICS LGYSILLMVT CTVYAFKTRG VPENFNEAKY IGFTMYTTC IVWLAFIPIF FGTAQSAEKL YIQTTTLTIS MNLSASVALG MLYMPKVYII IFHPELNVQK RKRSFKAVVT AATMSSRLSH KPSDRPNGE AKTELCENVD PNSPAAKKKY VSYNNLVI

UniProtKB: Metabotropic glutamate receptor 7

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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: 7.4
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: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 10.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498211
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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