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- PDB-25ty: Cryo-EM structure of the 2:2 mGlu7-ELFN1 complex in conformation B -

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Basic information

Entry
Database: PDB / ID: 25ty
TitleCryo-EM structure of the 2:2 mGlu7-ELFN1 complex in conformation B
Components
  • Metabotropic glutamate receptor 7
  • Protein ELFN1
KeywordsMEMBRANE PROTEIN / GPCR / Metabotropic glutamate receptor / ELFN1
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
GLUTAMIC ACID / Protein ELFN1 / Metabotropic glutamate receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLin, S. / Feng, Y. / Shui, S. / Chen, M. / Chu, X. / Yi, C. / Han, S. / Zhao, Q. / Wu, B.
Funding support China, 3items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Metabotropic glutamate receptor 7
C: Protein ELFN1
A: Metabotropic glutamate receptor 7
D: Protein ELFN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,44516
Polymers298,2494
Non-polymers4,19612
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 4 molecules BACD

#1: Protein Metabotropic glutamate receptor 7 / mGluR7


Mass: 103128.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM7, GPRC1G, MGLUR7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14831
#2: Protein Protein ELFN1 / Extracellular leucine-rich repeat and fibronectin type-III domain-containing protein 1 / Protein ...Extracellular leucine-rich repeat and fibronectin type-III domain-containing protein 1 / Protein phosphatase 1 regulatory subunit 28


Mass: 45995.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELFN1, PPP1R28 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0C7U0

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Sugars , 4 types, 10 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#7: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the mGlu7-ELFN1 complex in conformation C
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168491 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002110494
ELECTRON MICROSCOPYf_angle_d0.512614305
ELECTRON MICROSCOPYf_chiral_restr0.04281681
ELECTRON MICROSCOPYf_plane_restr0.0031860
ELECTRON MICROSCOPYf_dihedral_angle_d4.92751837

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