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- EMDB-36165: Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341... -

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Entry
Database: EMDB / ID: EMD-36165
TitleCryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495 (dimerization mode I)
Map data
Sample
  • Complex: mGlu2-3 heterodimer in presence of LY341495
    • Protein or peptide: Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A
    • Protein or peptide: Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR
  • Ligand: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex structure / mGlu2-3 heterodimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of cellular component organization / regulation of response to drug / group II metabotropic glutamate receptor activity / regulation of cellular response to stress / signaling receptor inhibitor activity / macrolide binding / activin receptor binding / TORC1 complex / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane ...regulation of cellular component organization / regulation of response to drug / group II metabotropic glutamate receptor activity / regulation of cellular response to stress / signaling receptor inhibitor activity / macrolide binding / activin receptor binding / TORC1 complex / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / intracellular glutamate homeostasis / behavioral response to nicotine / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of activin receptor signaling pathway / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / heart trabecula formation / glutamate receptor activity / I-SMAD binding / glutamate secretion / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / ventricular cardiac muscle tissue morphogenesis / regulation of glutamate secretion / long-term synaptic depression / protein maturation by protein folding / 'de novo' protein folding / postsynaptic modulation of chemical synaptic transmission / FK506 binding / regulation of dopamine secretion / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of immune response / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / heart morphogenesis / supramolecular fiber organization / regulation of synaptic transmission, glutamatergic / sarcoplasmic reticulum membrane / positive regulation of protein metabolic process / presynaptic modulation of chemical synaptic transmission / negative regulation of autophagy / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / response to cocaine / peptidylprolyl isomerase / G protein-coupled receptor activity / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / calcium ion transmembrane transport / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / positive regulation of protein binding / regulation of protein localization / presynaptic membrane / gene expression / protein refolding / G alpha (i) signalling events / scaffold protein binding / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / postsynaptic membrane / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / dendritic spine / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / axon / protein serine/threonine kinase activity / glutamatergic synapse / dendrite / protein-containing complex binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / GPCR, family 3, metabotropic glutamate receptor 2 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / GPCR, family 3, metabotropic glutamate receptor ...GPCR, family 3, metabotropic glutamate receptor 3 / GPCR, family 3, metabotropic glutamate receptor 2 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / GPCR, family 3, metabotropic glutamate receptor / : / Rapamycin binding domain / 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. / PIK-related kinase, FAT / FATC domain / GPCR, family 3 / FATC / FAT domain / G-protein coupled receptors family 3 profile. / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / : / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Phosphatidylinositol 3- and 4-kinase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A / Metabotropic glutamate receptor 2 / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang X / Wang M / Xu T / Feng Y / Zhao Q / Wu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
National Science Foundation (NSF, China)82121005 China
CitationJournal: Cell Res / Year: 2023
Title: Structural insights into dimerization and activation of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers.
Authors: Xinwei Wang / Mu Wang / Tuo Xu / Ye Feng / Qiang Shao / Shuo Han / Xiaojing Chu / Yechun Xu / Shuling Lin / Qiang Zhao / Beili Wu /
Abstract: Heterodimerization of the metabotropic glutamate receptors (mGlus) has shown importance in the functional modulation of the receptors and offers potential drug targets for treating central nervous ...Heterodimerization of the metabotropic glutamate receptors (mGlus) has shown importance in the functional modulation of the receptors and offers potential drug targets for treating central nervous system diseases. However, due to a lack of molecular details of the mGlu heterodimers, understanding of the mechanisms underlying mGlu heterodimerization and activation is limited. Here we report twelve cryo-electron microscopy (cryo-EM) structures of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers in different conformational states, including inactive, intermediate inactive, intermediate active and fully active conformations. These structures provide a full picture of conformational rearrangement of mGlu2-mGlu3 upon activation. The Venus flytrap domains undergo a sequential conformational change, while the transmembrane domains exhibit a substantial rearrangement from an inactive, symmetric dimer with diverse dimerization patterns to an active, asymmetric dimer in a conserved dimerization mode. Combined with functional data, these structures reveal that stability of the inactive conformations of the subunits and the subunit-G protein interaction pattern are determinants of asymmetric signal transduction of the heterodimers. Furthermore, a novel binding site for two mGlu4 positive allosteric modulators was observed in the asymmetric dimer interfaces of the mGlu2-mGlu4 heterodimer and mGlu4 homodimer, and may serve as a drug recognition site. These findings greatly extend our knowledge about signal transduction of the mGlus.
History
DepositionMay 12, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36165.png

Downloads & links

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Map

FileDownload / File: emd_36165.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.56 Å		1.07 Å/pix.
x 360 pix.
= 385.56 Å		1.07 Å/pix.
x 360 pix.
= 385.56 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8808835 - 3.4607553
Average (Standard dev.)0.0003267982 (±0.040029544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36165_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_36165_half_map_2.map
Projections & Slices
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Sample components

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Entire : mGlu2-3 heterodimer in presence of LY341495

EntireName: mGlu2-3 heterodimer in presence of LY341495
Components
  • Complex: mGlu2-3 heterodimer in presence of LY341495
    • Protein or peptide: Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A
    • Protein or peptide: Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR
  • Ligand: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mGlu2-3 heterodimer in presence of LY341495

SupramoleculeName: mGlu2-3 heterodimer in presence of LY341495 / 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 2,Peptidyl-prolyl cis-trans isome...

MacromoleculeName: Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A
type: protein_or_peptide / ID: 1
Details: Author stated 'all the data are processed in Cryosparc with default prameters, as all the other deposition. There should be no contamination.'
Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.398914 KDa
Recombinant expressionOrganism: mammal environmental sample (environmental samples)
SequenceString: DYKDDDDGAP EGPAKKVLTL EGDLVLGGLF PVHQKGGPAE DCGPVNEHRG IQRLEAMLFA LDRINRDPHL LPGVRLGAHI LDSCSKDTH ALEQALDFVR ASLSRGADGS RHICPDGSYA THGDAPTAIT GVIGGSYSDV SIQVANLLRL FQIPQISYAS T SAKLSDKS ...String:
DYKDDDDGAP EGPAKKVLTL EGDLVLGGLF PVHQKGGPAE DCGPVNEHRG IQRLEAMLFA LDRINRDPHL LPGVRLGAHI LDSCSKDTH ALEQALDFVR ASLSRGADGS RHICPDGSYA THGDAPTAIT GVIGGSYSDV SIQVANLLRL FQIPQISYAS T SAKLSDKS RYDYFARTVP PDFFQAKAMA EILRFFNWTY VSTVASEGDY GETGIEAFEL EARARNICVA TSEKVGRAMS RA AFEGVVR ALLQKPSARV AVLFTRSEDA RELLAASQRL NASFTWVASD GWGALESVVA GSEGAAEGAI TIELASYPIS DFA SYFQSL DPWNNSRNPW FREFWEQRFR CSFRQRDCAA HSLRAVPFEQ ESKIMFVVNA VYAMAHALHN MHRALCPNTT RLCD AMRPV NGRRLYKDFV LNVKFDAPFR PADTHNEVRF DRFGDGIGRY NIFTYLRAGS GRYRYQKVGY WAEGLTLDTS LIPWA SPSA GPLPASRCSE PCLQNEVKSV QPGEVCCWLC IPCQPYEYRL DEFTCADCGL GYWPNASLTG CFELPQEYIR WGDAWA VGP VTIACLGALA TLFVLGVFVR HNATPVVKAS GRELCYILLG GVFLCYCMTF IFIAKPSTAV CTLRRLGLGT AFSVCYS AL LTKTNRIARI FGGAREGAQR PRFISPASQV AICLALISGQ LLIVVAWLVV EAPGTGKETA PERREVVTLR CNHRDASM L GSLAYNVLLI ALCTLYAFKT RKCPENFNEA KFIGFTMYTT CIIWLAFLPI FYVTSSDYRV QTTTMCVSVS LSGSVVLGC LFAPKLHIIL FQPQKNVVSH RAPTSRFGSA AARASSSLGQ GSGSQFVPTV CNGREVVDST TSSLLEVLFQ GPGVQVETIS PGDGRTFPK RGQTCVVHYT GMLEDGKKFD SSRDRNKPFK FMLGKQEVIR GWEEGVAQMS VGQRAKLTIS PDYAYGATGH P GIIPPHAT LVFDVELLKL EFAAAHHHHH HHHHH

UniProtKB: Metabotropic glutamate receptor 2, Peptidyl-prolyl cis-trans isomerase FKBP1A

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Macromolecule #2: Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR

MacromoleculeName: Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 112.712961 KDa
Recombinant expressionOrganism: mammal environmental sample (environmental samples)
SequenceString: DYKDDDDKGA PWSHPQFEKG SGSWSHPQFE KLGDHNFLRR EIKIEGDLVL GGLFPINEKG TGTEECGRIN EDRGIQRLEA MLFAIDEIN KDDYLLPGVK LGVHILDTCS RDTYALEQSL EFVRASLTKV DEAEYMCPDG SYAIQENIPL LIAGVIGGSY S SVSIQVAN ...String:
DYKDDDDKGA PWSHPQFEKG SGSWSHPQFE KLGDHNFLRR EIKIEGDLVL GGLFPINEKG TGTEECGRIN EDRGIQRLEA MLFAIDEIN KDDYLLPGVK LGVHILDTCS RDTYALEQSL EFVRASLTKV DEAEYMCPDG SYAIQENIPL LIAGVIGGSY S SVSIQVAN LLRLFQIPQI SYASTSAKLS DKSRYDYFAR TVPPDFYQAK AMAEILRFFN WTYVSTVASE GDYGETGIEA FE QEARLRN ICIATAEKVG RSNIRKSYDS VIRELLQKPN ARVVVLFMRS DDSRELIAAA SRANASFTWV ASDGWGAQES IIK GSEHVA YGAITLELAS QPVRQFDRYF QSLNPYNNHR NPWFRDFWEQ KFQCSLQNKR NHRRVCDKHL AIDSSNYEQE SKIM FVVNA VYAMAHALHK MQRTLCPNTT KLCDAMKILD GKKLYKDYLL KINFTAPFNP NKDADSIVKF DTFGDGMGRY NVFNF QNVG GKYSYLKVGH WAETLSLDVN SIHWSRNSVP TSQCSDPCAP NEMKNMQPGD VCCWICIPCE PYEYLADEFT CMDCGS GQW PTADLTGCYD LPEDYIRWED AWAIGPVTIA CLGFMCTCMV VTVFIKHNNT PLVKASGREL CYILLFGVGL SYCMTFF FI AKPSPVICAL RRLGLGSSFA ICYSALLTKT NCIARIFDGV KNGAQRPKFI SPSSQVFICL GLILVQIVMV SVWLILEA P GTRRYTLAEK RETVILKCNV KDSSMLISLT YDVILVILCT VYAFKTRKCP ENFNEAKFIG FTMYTTCIIW LAFLPIFYV TSSDYRVQTT TMCISVSLSG FVVLGCLFAP KVHIILFQPQ KNVVTHRLHL NRFSVSGTGT TYSQSSASTY VPTVCNGREV LDSTTSSLL EVLFQGPAIL WHEMWHEGLE EASRLYFGER NVKGMFEVLE PLHAMMERGP QTLKETSFNQ AYGRDLMEAQ E WCRKYMKS GNVKDLTQAW DLYYHVFRRI SKQEF

UniProtKB: Metabotropic glutamate receptor 3, Serine/threonine-protein kinase mTOR

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Macromolecule #3: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine

MacromoleculeName: 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine
type: ligand / ID: 3 / Number of copies: 2 / Formula: Z99
Molecular weightTheoretical: 353.369 Da
Chemical component information

ChemComp-Z99:
2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine / antidepressant, antagonist*YM

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 512450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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