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- EMDB-60588: Cryo-EM Structure of the 2:2 Complex of mGlu3 and beta-arrestin1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60588
TitleCryo-EM Structure of the 2:2 Complex of mGlu3 and beta-arrestin1
Map datacomposite map combined from focus-refined maps
Sample
  • Complex: GPCR/beta-arrestin/scFv30 complex
    • Protein or peptide: Metabotropic glutamate receptor 3
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: CHOLESTEROL
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / G protein-coupled receptor internalization / arrestin family protein binding ...group II metabotropic glutamate receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / G protein-coupled receptor internalization / arrestin family protein binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / Golgi Associated Vesicle Biogenesis / stress fiber assembly / cellular response to stress / positive regulation of Rho protein signal transduction / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / enzyme inhibitor activity / negative regulation of Notch signaling pathway / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / Activated NOTCH1 Transmits Signal to the Nucleus / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / calcium channel regulator activity / G protein-coupled receptor binding / G protein-coupled receptor activity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / endocytic vesicle membrane / positive regulation of protein phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Cargo recognition for clathrin-mediated endocytosis / Signaling by BRAF and RAF1 fusions / Clathrin-mediated endocytosis / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / presynaptic membrane / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / scaffold protein binding / G alpha (i) signalling events / G alpha (s) signalling events / molecular adaptor activity / chemical synaptic transmission / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / gene expression / postsynaptic membrane / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / Ub-specific processing proteases / protein ubiquitination / postsynaptic density / nuclear body / Golgi membrane / axon / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain ...GPCR, family 3, metabotropic glutamate receptor 3 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / GPCR, family 3, metabotropic glutamate receptor / : / Arrestin-like, C-terminal / 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 / G-protein coupled receptors family 3 signature 3. / 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 / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Immunoglobulin E-set
Similarity search - Domain/homology
Beta-arrestin-1 / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWen TL / Du M / Yang X / Shen YQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Molecular basis of β-arrestin coupling to the metabotropic glutamate receptor mGlu3.
Authors: Tianlei Wen / Mei Du / Yue Lu / Nan Jia / Xuhang Lu / Ning Liu / Shenghai Chang / Xing Zhang / Yuequan Shen / Xue Yang /
Abstract: β-Arrestins (βarrs) mediate the desensitization and internalization of activated G-protein-coupled receptors (GPCRs). The molecular mechanism by which dimeric family C GPCR members recruit ...β-Arrestins (βarrs) mediate the desensitization and internalization of activated G-protein-coupled receptors (GPCRs). The molecular mechanism by which dimeric family C GPCR members recruit arrestins remains elusive. Here we report two structures of metabotropic glutamate receptor subtype 3 (mGlu3) coupled to βarr1, with stoichiometries of 2:1 and 2:2. The L-glutamate-bound mGlu3 dimer adopts an inactive state, with both Venus flytrap domains closed, engaging βarr1 either asymmetrically or symmetrically. The transmembrane domain of the mGlu3 protomer interacts with βarr1 through a binding pocket formed by three intracellular loops and an ordered C-terminal region. Three phosphorylation sites (pS857, pS859 and pT860) on the C-terminal tail of mGlu3 engage the N domain of βarr1. βarr1 stabilizes mGlu3 in an inactive conformation, characterized by a TM3/TM4-TM3/TM4 dimeric interface, previously observed in the negative allosteric modulator-bound structure of mGlu3. Our findings provide important insights into βarr-mediated inactivation of family C GPCRs.
History
DepositionJun 18, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60588.png

Downloads & links

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Map

FileDownload / File: emd_60588.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map combined from focus-refined maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.15066648 - 1.8717974
Average (Standard dev.)0.008001901 (±0.02755221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : GPCR/beta-arrestin/scFv30 complex

EntireName: GPCR/beta-arrestin/scFv30 complex
Components
  • Complex: GPCR/beta-arrestin/scFv30 complex
    • Protein or peptide: Metabotropic glutamate receptor 3
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: CHOLESTEROL

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Supramolecule #1: GPCR/beta-arrestin/scFv30 complex

SupramoleculeName: GPCR/beta-arrestin/scFv30 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: Metabotropic glutamate receptor 3

MacromoleculeName: Metabotropic glutamate receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.301766 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKMLTRLQVL TLALFSKGFL LSLGDHNFLR REIKIEGDLV LGGLFPINEK GTGTEECGRI NEDRGIQRLE AMLFAIDEIN KDDYLLPGV KLGVHILDTC SRDTYALEQS LEFVRASLTK VDEAEYMCPD GSYAIQENIP LLIAGVIGGS YSSVSIQVAN L LRLFQIPQ ...String:
MKMLTRLQVL TLALFSKGFL LSLGDHNFLR REIKIEGDLV LGGLFPINEK GTGTEECGRI NEDRGIQRLE AMLFAIDEIN KDDYLLPGV KLGVHILDTC SRDTYALEQS LEFVRASLTK VDEAEYMCPD GSYAIQENIP LLIAGVIGGS YSSVSIQVAN L LRLFQIPQ ISYASTSAKL SDKSRYDYFA RTVPPDFYQA KAMAEILRFF NWTYVSTVAS EGDYGETGIE AFEQEARLRN IC IATAEKV GRSNIRKSYD SVIRELLQKP NARVVVLFMR SDDSRELIAA ASRANASFTW VASDGWGAQE SIIKGSEHVA YGA ITLELA SQPVRQFDRY FQSLNPYNNH RNPWFRDFWE QKFQCSLQNK RNHRRVCDKH LAIDSSNYEQ ESKIMFVVNA VYAM AHALH KMQRTLCPNT TKLCDAMKIL DGKKLYKDYL LKINFTAPFN PNKDADSIVK FDTFGDGMGR YNVFNFQNVG GKYSY LKVG HWAETLSLDV NSIHWSRNSV PTSQCSDPCA PNEMKNMQPG DVCCWICIPC EPYEYLADEF TCMDCGSGQW PTADLT GCY DLPEDYIRWE DAWAIGPVTI ACLGFMCTCM VVTVFIKHNN TPLVKASGRE LCYILLFGVG LSYCMTFFFI AKPSPVI CA LRRLGLGSSF AICYSALLTK TNCIARIFDG VKNGAQRPKF ISPSSQVFIC LGLILVQIVM VSVWLILEAP GTRRYTLA E KRETVILKCN VKDSSMLISL TYDVILVILC TVYAFKTRKC PENFNEAKFI GFTMYTTCII WLAFLPIFYV TSSDYRVQT TTMCISVSLS GFVVLGCLFA PKVHIILFQP QKNVVTHRLH LNRFSVSGTG TTYSQ(SEP)(SEP)A(SEP)(TPO) YVPT VCNGR EVLDSTTSSL

UniProtKB: Metabotropic glutamate receptor 3

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Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.067332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTVA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA LGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTVA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA LGVDYEVKAF VAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD IVLFNTA QYKVPVAMEE ADDTVAPSST FSKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL IELDTNDDDI VFEDFARQRL KGMK DDKEE EEDGTGSPQL NNR

UniProtKB: Beta-arrestin-1

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Macromolecule #3: scFv30

MacromoleculeName: scFv30 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.986742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG LEWVASISSY YGYTYYADSV KGRFTISADT SKNTAYLQMN SLRAEDTAVY YCARSRQFWY SGLDYWGQGT LV TVSSAHH HHHH

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Macromolecule #5: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CtfFind 4.1.8 / Type: NONE
Startup modelType of model: NONE / Details: Ab-initio reconstruction by CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51324
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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