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- EMDB-31237: Cryo-EM structure of inactive mGlu7 homodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-31237
TitleCryo-EM structure of inactive mGlu7 homodimer
Map data
Sample
  • Complex: Inactive mGlu7 homodimer
    • Protein or peptide: Isoform 3 of Metabotropic glutamate receptor 7
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 / negative regulation of glutamate secretion / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / 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 / negative regulation of glutamate secretion / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / glutamate binding / presynaptic active zone / plasma membrane => GO:0005886 / asymmetric synapse / regulation of synaptic transmission, glutamatergic / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / PDZ domain binding / sensory perception of sound / cell cortex / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / membrane => GO:0016020 / receptor complex / G protein-coupled receptor signaling pathway / axon / dendrite / calcium ion binding / 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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / 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: 4.0 Å
AuthorsDu J / Wang D / Fan H / Tai L / Lin S / Han S / Sun F / Wu B / Zhao Q
Funding support China, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
National Science Foundation (NSF, China)81525024 China
National Science Foundation (NSF, China)31830020 China
National Science Foundation (NSF, China)81720108031 China
CitationJournal: Nature / Year: 2021
Title: Structures of human mGlu2 and mGlu7 homo- and heterodimers.
Authors: Juan Du / Dejian Wang / Hongcheng Fan / Chanjuan Xu / Linhua Tai / Shuling Lin / Shuo Han / Qiuxiang Tan / Xinwei Wang / Tuo Xu / Hui Zhang / Xiaojing Chu / Cuiying Yi / Peng Liu / Xiaomei ...Authors: Juan Du / Dejian Wang / Hongcheng Fan / Chanjuan Xu / Linhua Tai / Shuling Lin / Shuo Han / Qiuxiang Tan / Xinwei Wang / Tuo Xu / Hui Zhang / Xiaojing Chu / Cuiying Yi / Peng Liu / Xiaomei Wang / Yu Zhou / Jean-Philippe Pin / Philippe Rondard / Hong Liu / Jianfeng Liu / Fei Sun / Beili Wu / Qiang Zhao /
Abstract: The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmission and neuronal excitability in the central nervous system. These receptors probably exist as both ...The metabotropic glutamate receptors (mGlus) are involved in the modulation of synaptic transmission and neuronal excitability in the central nervous system. These receptors probably exist as both homo- and heterodimers that have unique pharmacological and functional properties. Here we report four cryo-electron microscopy structures of the human mGlu subtypes mGlu2 and mGlu7, including inactive mGlu2 and mGlu7 homodimers; mGlu2 homodimer bound to an agonist and a positive allosteric modulator; and inactive mGlu2-mGlu7 heterodimer. We observed a subtype-dependent dimerization mode for these mGlus, as a unique dimer interface that is mediated by helix IV (and that is important for limiting receptor activity) exists only in the inactive mGlu2 structure. The structures provide molecular details of the inter- and intra-subunit conformational changes that are required for receptor activation, which distinguish class C G-protein-coupled receptors from those in classes A and B. Furthermore, our structure and functional studies of the mGlu2-mGlu7 heterodimer suggest that the mGlu7 subunit has a dominant role in controlling dimeric association and G-protein activation in the heterodimer. These insights into mGlu homo- and heterodimers highlight the complex landscape of mGlu dimerization and activation.
History
DepositionApr 26, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7epc
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31237.png

Downloads & links

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Map

FileDownload / File: emd_31237.map.gz / Format: CCP4 / Size: 181 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.02894926 - 0.10321174
Average (Standard dev.)0.00031037728 (±0.0016452839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-1
Dimensions362362362
Spacing362362362
CellA=B=C: 289.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.80.80.8
M x/y/z362362362
origin x/y/z0.0000.0000.000
length x/y/z289.600289.600289.600
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS-1-1-1
NC/NR/NS362362362
D min/max/mean-0.0290.1030.000

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Supplemental data

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Sample components

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Entire : Inactive mGlu7 homodimer

EntireName: Inactive mGlu7 homodimer
Components
  • Complex: Inactive mGlu7 homodimer
    • Protein or peptide: Isoform 3 of Metabotropic glutamate receptor 7

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Supramolecule #1: Inactive mGlu7 homodimer

SupramoleculeName: Inactive mGlu7 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: mammal environmental sample (environmental samples)

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Macromolecule #1: Isoform 3 of Metabotropic glutamate receptor 7

MacromoleculeName: Isoform 3 of Metabotropic glutamate receptor 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.276977 KDa
Recombinant expressionOrganism: mammal environmental sample (environmental samples)
SequenceString: GAPQEMYAPH SIRIEGDVTL GGLFPVHAKG PSGVPCGDIK RENGIHRLEA MLYALDQINS DPNLLPNVTL GARILDTCSR DTYALEQSL TFVQALIQKD TSDVRCTNGE PPVFVKPEKV VGVIGASGSS VSIMVANILR LFQIPQISYA STAPELSDDR R YDFFSRVV ...String:
GAPQEMYAPH SIRIEGDVTL GGLFPVHAKG PSGVPCGDIK RENGIHRLEA MLYALDQINS DPNLLPNVTL GARILDTCSR DTYALEQSL TFVQALIQKD TSDVRCTNGE PPVFVKPEKV VGVIGASGSS VSIMVANILR LFQIPQISYA STAPELSDDR R YDFFSRVV PPDSFQAQAM VDIVKALGWN YVSTLASEGS YGEKGVESFT QISKEAGGLC IAQSVRIPQE RKDRTIDFDR II KQLLDTP NSRAVVIFAN DEDIKQILAA AKRADQVGHF LWVGSDSWGS KINPLHQHED IAEGAITIQP KRATVEGFDA YFT SRTLEN NRRNVWFAEY WEENFNCKLT ISGSKKEDTD RKCTGQERIG KDSNYEQEGK VQFVIDAVYA MAHALHHMNK DLCA DYRGV CPEMEQAGGK KLLKYIRNVN FNGSAGTPVM FNKNGDAPGR YDIFQYQTTN TSNPGYRLIG QWTDELQLNI EDMQW GKGV REIPASVCTL PCKPGQRKKT QKGTPCCWTC EPCDGYQYQF DEMTCQHCPY DQRPNENRTG CQDIPIIKLE WHSPWA VIP VFLAMLGIIA TIFVMATFIR YNDTPIVRAS GRELSYVLLT GIFLCYIITF LMIAKPDVAV CSFRRVFLGL GMCISYA AL LTKTYRIYRI FEQGKKSVTA PRLISPTSQL AITSSLISVQ LLGVFIWFIV DPPNIIIDYD EHKTMNPEQA RGVLKCDI T DLQIICSLGY SILLMVTCTV YAFKTRGVPE NFNEAKYIGF TMYTTCIVWL AFIPIFFGTA QSAEKLYIQT TTLTISMNL SASVALGMLY MPKVYIIIFH PELNVQKREF LEVLFQGPGS GSWSHPQFEK DYKDDDD

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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

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.47 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1011214

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