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- EMDB-72409: Metabotropic Glutamate Receptor 7 in complex with ecto-domain of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72409
TitleMetabotropic Glutamate Receptor 7 in complex with ecto-domain of Extracellular Leucine Rich Repeat and Fibronectin Type III Domain Containing 2
Map data
Sample
  • Complex: Complex of mGluR7 and ecto-domain of ELFN2
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 29
    • Protein or peptide: Metabotropic glutamate receptor 7
KeywordsmGluR7 / ELFN2 / GPCR / glutamate / trans-synaptic / MEMBRANE PROTEIN
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / negative regulation of glutamate secretion / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / serine binding / synaptic membrane adhesion / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding ...group III metabotropic glutamate receptor activity / negative regulation of glutamate secretion / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / serine binding / synaptic membrane adhesion / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding / protein phosphatase inhibitor activity / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / adenylate cyclase inhibitor activity / sensory perception of sound / dendritic shaft / PDZ domain binding / establishment of protein localization / postsynaptic density membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / signaling receptor activity / chemical synaptic transmission / cell cortex / G alpha (i) signalling events / signaling receptor complex / postsynaptic membrane / protein dimerization activity / axon / calcium ion binding / dendrite / : / membrane / plasma membrane
Similarity search - Function
: / ELFN1/ELFN2, fibronectin type-III domain / 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 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain ...: / ELFN1/ELFN2, fibronectin type-III domain / 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 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Receptor, ligand binding region / Receptor family ligand binding region / Leucine-rich repeat domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic glutamate receptor 7 / Protein phosphatase 1 regulatory subunit 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLudlam WG / Chang CT / Liauw BW / Cho HJ / Sawh-Gopal A / Izard T / Bao H / Dunn HA / Vafabakhsh R / Martemyanov KA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA056414 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS124758 United States
CitationJournal: To Be Published
Title: Structural basis for modulation of group III mGlu receptors by trans-synaptic interactions
Authors: Ludlam WG / Chang CT / Liauw BW / Cho HJ / Sawh-Gopal A / Izard T / Bao H / Dunn HA / Vafabakhsh R / Martemyanov KA
History
DepositionSep 1, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72409.png

Downloads & links

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Map

FileDownload / File: emd_72409.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.41431254 - 0.8606573
Average (Standard dev.)0.0044872276 (±0.027575722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72409_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72409_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 : Complex of mGluR7 and ecto-domain of ELFN2

EntireName: Complex of mGluR7 and ecto-domain of ELFN2
Components
  • Complex: Complex of mGluR7 and ecto-domain of ELFN2
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 29
    • Protein or peptide: Metabotropic glutamate receptor 7

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Supramolecule #1: Complex of mGluR7 and ecto-domain of ELFN2

SupramoleculeName: Complex of mGluR7 and ecto-domain of ELFN2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein phosphatase 1 regulatory subunit 29

MacromoleculeName: Protein phosphatase 1 regulatory subunit 29 / type: protein_or_peptide / ID: 1
Details: M1-A22 is cleaved off signal peptide. D23-G248 is leucine rich repeat domain. S249-T379 is not resolved in the structure. L380-Q385 is human rhinovirus C3 protease cut site sequence.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.056125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLRLGLCAAA LLCVCRPGAV RADCWLIEGD KGYVWLAICS QNQPPYETIP QHINSTVHDL RLNENKLKAV LYSSLNRFGN LTDLNLTKN EISYIEDGAF LGQSSLQVLQ LGYNKLSNLT EGMLRGMSRL QFLFVQHNLI EVVTPTAFSE CPSLISIDLS S NRLSRLDG ...String:
MLRLGLCAAA LLCVCRPGAV RADCWLIEGD KGYVWLAICS QNQPPYETIP QHINSTVHDL RLNENKLKAV LYSSLNRFGN LTDLNLTKN EISYIEDGAF LGQSSLQVLQ LGYNKLSNLT EGMLRGMSRL QFLFVQHNLI EVVTPTAFSE CPSLISIDLS S NRLSRLDG ATFASLASLM VCELAGNPFN CECDLFGFLA WLVVFNNVTK NYDRLQCESP REFAGYPLLV PRPYHSLNAI TV LQAKCRN GSLPARPVSH PTPYSTDAQR EPDENSGFNP DEILSVEPPA SSTTDASAGP AIKLHHVTFT SATLVVIIPH PYS KMYILV QYNNSYFSDV MTLKNKKEIV TLDKLRAHTE YTFCVTSLRN SRRFNHTCLT FTTLEVLFQ

UniProtKB: Protein phosphatase 1 regulatory subunit 29

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Macromolecule #2: Metabotropic glutamate receptor 7

MacromoleculeName: Metabotropic glutamate receptor 7 / type: protein_or_peptide / ID: 2
Details: M1-G34 is cleaved signal peptide. Q35-M37 is not resolved in structure. Y38-S521 is Venus Flytrap domain. V522-R859 is not resolved in structure. L860-Q865 is human rhinovirus C3 protease cut site sequence.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.154852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVQLRKLLRV LTLMKFPCCV LEVLLCALAA AARGQEMYAP HSIRIEGDVT LGGLFPVHAK GPSGVPCGDI KRENGIHRLE AMLYALDQI NSDPNLLPNV TLGARILDTC SRDTYALEQS LTFVQALIQK DTSDVRCTNG EPPVFVKPEK VVGVIGASGS S VSIMVANI ...String:
MVQLRKLLRV LTLMKFPCCV LEVLLCALAA AARGQEMYAP HSIRIEGDVT LGGLFPVHAK GPSGVPCGDI KRENGIHRLE AMLYALDQI NSDPNLLPNV TLGARILDTC SRDTYALEQS LTFVQALIQK DTSDVRCTNG EPPVFVKPEK VVGVIGASGS S VSIMVANI LRLFQIPQIS YASTAPELSD DRRYDFFSRV VPPDSFQAQA MVDIVKALGW NYVSTLASEG SYGEKGVESF TQ ISKEAGG LCIAQSVRIP QERKDRTIDF DRIIKQLLDT PNSRAVVIFA NDEDIKQILA AAKRADQVGH FLWVGSDSWG SKI NPLHQH EDIAEGAITI QPKRATVEGF DAYFTSRTLE NNRRNVWFAE YWEENFNCKL TISGSKKEDT DRKCTGQERI GKDS NYEQE GKVQFVIDAV YAMAHALHHM NKDLCADYRG VCPEMEQAGG KKLLKYIRNV NFNGSAGTPV MFNKNGDAPG RYDIF QYQT TNTSNPGYRL IGQWTDELQL NIEDMQWGKG VREIPASVCT LPCKPGQRKK TQKGTPCCWT CEPCDGYQYQ FDEMTC QHC PYDQRPNENR TGCQDIPIIK LEWHSPWAVI PVFLAMLGII ATIFVMATFI RYNDTPIVRA SGRELSYVLL TGIFLCY II TFLMIAKPDV AVCSFRRVFL GLGMCISYAA LLTKTYRIYR IFEQGKKSVT APRLISPTSQ LAITSSLISV QLLGVFIW F IVDPPNIIID YDEHKTMNPE QARGVLKCDI TDLQIICSLG YSILLMVTCT VYAFKTRGVP ENFNEAKYIG FTMYTTCIV WLAFIPIFFG TAQSAEKLYI QTTTLTISMN LSASVALGML YMPKVYIIIF HPELNVQKRL EVLFQ

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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28023
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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