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- PDB-9y2f: Metabotropic Glutamate Receptor 7 in complex with ecto-domain of ... -

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Basic information

Entry
Database: PDB / ID: 9y2f
TitleMetabotropic Glutamate Receptor 7 in complex with ecto-domain of Extracellular Leucine Rich Repeat and Fibronectin Type III Domain Containing 2
Components
  • Metabotropic glutamate receptor 7
  • Protein phosphatase 1 regulatory subunit 29
KeywordsMEMBRANE PROTEIN / mGluR7 / ELFN2 / GPCR / glutamate / trans-synaptic
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 / protein phosphatase inhibitor activity / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / sensory perception of sound / adenylate cyclase inhibitor activity / dendritic shaft / establishment of protein localization / PDZ domain binding / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLudlam, W.G. / Chang, C.T. / Liauw, B.W. / Cho, H.J. / Sawh-Gopal, A. / Izard, T. / Bao, H. / Dunn, H.A. / Vafabakhsh, R. / Martemyanov, K.A.
Funding support United States, 2items
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: Sci Adv / Year: 2026
Title: Structural basis for modulation of group III mGlu receptors by transsynaptic interactions.
Authors: William G Ludlam / Chu-Ting Chang / Kristina Cechova / Brandon W Liauw / Hwa-Jin Cho / Safoura Salar / Anjelique Sawh-Gopal / Afroza Parvin / Simrat K Dhaliwal / Simran K Dhaliwal / Tina ...Authors: William G Ludlam / Chu-Ting Chang / Kristina Cechova / Brandon W Liauw / Hwa-Jin Cho / Safoura Salar / Anjelique Sawh-Gopal / Afroza Parvin / Simrat K Dhaliwal / Simran K Dhaliwal / Tina Izard / Huan Bao / Anne M Brown / Henry A Dunn / Reza Vafabakhsh / Kirill A Martemyanov /
Abstract: Group III metabotropic glutamate receptors (mGluRs) are critical signaling molecules that regulate strength, homeostasis, and plasticity of glutamatergic synaptic signaling. These receptors are ...Group III metabotropic glutamate receptors (mGluRs) are critical signaling molecules that regulate strength, homeostasis, and plasticity of glutamatergic synaptic signaling. These receptors are engaged in transsynaptic interactions with extracellular leucine-rich repeat and fibronectin type III domain-containing (ELFN) cell adhesion proteins. ELFN proteins have been shown to play a critical role in regulation of activity and localization of mGluRs activity in vivo, yet the exact nature of their regulatory interaction has remained unknown. Here, we present a cryo-electron microscopy structure of the ELFN-mGluR complex. We identify a specific ELFN-binding pocket on mGluRs involved in its allosteric regulation through the network of residues affecting the orthosteric ligand binding site. We further uncover cooperativity whereby mGluR activation increases their association with ELFN proteins as a potential feedback mechanism to regulate synaptic strength. Last, we determine that disruption in mGluR-ELFN interaction is a recurring mechanism underlying several neurological conditions as we delineate their structure-functional etiology.
History
DepositionSep 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein phosphatase 1 regulatory subunit 29
A: Metabotropic glutamate receptor 7
D: Protein phosphatase 1 regulatory subunit 29
B: Metabotropic glutamate receptor 7


Theoretical massNumber of molelcules
Total (without water)280,4224
Polymers280,4224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein phosphatase 1 regulatory subunit 29 / Extracellular leucine-rich repeat and fibronectin type III domain-containing protein 2 / Leucine- ...Extracellular leucine-rich repeat and fibronectin type III domain-containing protein 2 / Leucine-rich repeat and fibronectin type-III domain-containing protein 6 / Leucine-rich repeat-containing protein 62


Mass: 43056.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Gene: ELFN2, KIAA1904, LRRC62, PPP1R29 / Production host: Homo sapiens (human) / References: UniProt: Q5R3F8
#2: Protein Metabotropic glutamate receptor 7 / mGluR7


Mass: 97154.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM7, GPRC1G, MGLUR7 / Production host: Homo sapiens (human) / References: UniProt: Q14831
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: Complex of mGluR7 and ecto-domain of ELFN2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28023 / Symmetry type: POINT
RefinementHighest resolution: 4.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311156
ELECTRON MICROSCOPYf_angle_d0.53315160
ELECTRON MICROSCOPYf_dihedral_angle_d4.3211530
ELECTRON MICROSCOPYf_chiral_restr0.041686
ELECTRON MICROSCOPYf_plane_restr0.0042000

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