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- EMDB-80373: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-80373
TitleCryo-EM structure of the 2:1 mGlu7-ELFN1 complex
Map data
Sample
  • Complex: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex
    • Protein or peptide: Metabotropic glutamate receptor 7
    • Protein or peptide: Protein ELFN1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGPCR / Metabotropic glutamate receptor / ELFN1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of glutamate secretion / group III metabotropic glutamate receptor activity / 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 ...negative regulation of glutamate secretion / group III metabotropic glutamate receptor activity / 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 / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / sensory perception of sound / adenylate cyclase inhibitor activity / excitatory synapse / dendritic shaft / PDZ domain binding / establishment of protein localization / synapse organization / 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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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
Protein ELFN1 / Metabotropic glutamate receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLin S / Feng Y / Shui S / Chen M / Chu X / Yi C / Han S / Zhao Q / Wu B
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32530052 China
National Science Foundation (NSF, China)32400997 China
National Science Foundation (NSF, China)82121005 China
CitationJournal: To be published
Title: Structural basis for the synaptic adhesion protein ELFN1-mediated modulation of mGlu7
Authors: Lin S / Feng Y / Shui S / Chen M / Chu X / Yi C / Han S / Zhao Q / Wu B
History
DepositionApr 17, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80373.png

Downloads & links

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Map

FileDownload / File: emd_80373.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.)
1.07 Å/pix.
x 400 pix.
= 428.4 Å		1.07 Å/pix.
x 400 pix.
= 428.4 Å		1.07 Å/pix.
x 400 pix.
= 428.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.0583491 - 1.9305156
Average (Standard dev.)-0.00013329745 (±0.026803872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80373_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_80373_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 : Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex

EntireName: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex
Components
  • Complex: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex
    • Protein or peptide: Metabotropic glutamate receptor 7
    • Protein or peptide: Protein ELFN1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex

SupramoleculeName: Cryo-EM structure of the 2:1 mGlu7-ELFN1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 103.128602 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDGSW SHPQFEKGSG SWSHPQFEKG SSENLYFQSQ EMYAPHSIRI EGDVTLGGLF PVHAKGPSGV PCGDIKRENG IHRLEAMLY ALDQINSDPN LLPNVTLGAR ILDTCSRDTY ALEQSLTFVQ ALIQKDTSDV RCTNGEPPVF VKPEKVVGVI G ASGSSVSI ...String:
DYKDDDDGSW SHPQFEKGSG SWSHPQFEKG SSENLYFQSQ EMYAPHSIRI EGDVTLGGLF PVHAKGPSGV PCGDIKRENG IHRLEAMLY ALDQINSDPN LLPNVTLGAR ILDTCSRDTY ALEQSLTFVQ ALIQKDTSDV RCTNGEPPVF VKPEKVVGVI G ASGSSVSI MVANILRLFQ IPQISYASTA PELSDDRRYD FFSRVVPPDS FQAQAMVDIV KALGWNYVST LASEGSYGEK GV ESFTQIS KEAGGLCIAQ SVRIPQERKD RTIDFDRIIK QLLDTPNSRA VVIFANDEDI KQILAAAKRA DQVGHFLWVG SDS WGSKIN PLHQHEDIAE GAITIQPKRA TVEGFDAYFT SRTLENNRRN VWFAEYWEEN FNCKLTISGS KKEDTDRKCT GQER IGKDS NYEQEGKVQF VIDAVYAMAH ALHHMNKDLC ADYRGVCPEM EQAGGKKLLK YIRNVNFNGS AGTPVMFNKN GDAPG RYDI FQYQTTNTSN PGYRLIGQWT DELQLNIEDM QWGKGVREIP ASVCTLPCKP GQRKKTQKGT PCCWTCEPCD GYQYQF DEM TCQHCPYDQR PNENRTGCQD IPIIKLEWHS PWAVIPVFLA MLGIIATIFV MATFIRYNDT PIVRASGREL SYVLLTG IF LCYIITFLMI AKPDVAVCSF RRVFLGLGMC ISYAALLTKT NRIYRIFEQG KKSVTAPRLI SPTSQLAITS SLISVQLL G VFIWFGVDPP NIIIDYDEHK TMNPEQARGV LKCDITDLQI ICSLGYSILL MVTCTVYAIK TRGVPENFNE AKPIGFTMY TTCIVWLAFI PIFFGTAQSA EKLYIQTTTL TISMNLSASV ALGMLYMPKV YIIIFHPELN VQKRKRSFKA VVTAATMSSR LSHKPSDRP NGEAKTELCE NVDPNSPAAK KKYVSYNNLV I

UniProtKB: Metabotropic glutamate receptor 7

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Macromolecule #2: Protein ELFN1

MacromoleculeName: Protein ELFN1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.995973 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DCWLIEGDKG FVWLAICSQN QPPYEAIPQQ INSTIVDLRL NENRIRSVQY ASLSRFGNLT YLNLTKNEIG YIEDGAFSGQ FNLQVLQLG YNRLRNLTEG MLRGLGKLEY LYLQANLIEV VMASSFWECP NIVNIDLSMN RIQQLNSGTF AGLAKLSVCE L YSNPFYCS ...String:
DCWLIEGDKG FVWLAICSQN QPPYEAIPQQ INSTIVDLRL NENRIRSVQY ASLSRFGNLT YLNLTKNEIG YIEDGAFSGQ FNLQVLQLG YNRLRNLTEG MLRGLGKLEY LYLQANLIEV VMASSFWECP NIVNIDLSMN RIQQLNSGTF AGLAKLSVCE L YSNPFYCS CELLGFLRWL AAFTNATQTY DRMQCESPPV YSGYYLLGQG RRGHRSILSK LQSVCTEDSY AAEVVGPPRP AS GRSQPGR SPPPPPPPEP SDMPCADDEC FSGDGTTPLV ALPTLATQAE ARPLIKVKQL TQNSATITVQ LPSPFHRMYT LEH FNNSKA STVSRLTKAQ EEIRLTNLFT LTNYTYCVVS TSAGLRHNHT CLTICLPRLP SPPGPVPSPS TATHYEFLEV LFQG PHHHH HHHHHH

UniProtKB: Protein ELFN1

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7epc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64331
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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