[English] 日本語
Yorodumi
- EMDB-60589: Cryo-EM Structure of the 2:1 Complex of mGlu3 and beta-arrestin1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60589
TitleCryo-EM Structure of the 2:1 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 / G protein-coupled glutamate receptor signaling pathway / negative regulation of adenylate cyclase activity / astrocyte projection / G protein-coupled receptor internalization / Class C/3 (Metabotropic glutamate/pheromone receptors) ...group II metabotropic glutamate receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled glutamate receptor signaling pathway / negative regulation of adenylate cyclase activity / astrocyte projection / G protein-coupled receptor internalization / Class C/3 (Metabotropic glutamate/pheromone receptors) / arrestin family protein binding / glutamate receptor activity / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cellular response to stress / positive regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / negative regulation of NF-kappaB transcription factor activity / pseudopodium / negative regulation of interleukin-6 production / enzyme inhibitor activity / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / clathrin-coated pit / insulin-like growth factor receptor binding / calcium channel regulator activity / negative regulation of protein ubiquitination / cytoplasmic vesicle membrane / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / G protein-coupled receptor activity / 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 / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / presynaptic membrane / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / scaffold protein binding / G alpha (i) signalling events / G alpha (s) signalling events / gene expression / chemical synaptic transmission / molecular adaptor activity / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynaptic membrane / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / Ub-specific processing proteases / protein ubiquitination / nuclear body / axon / Golgi membrane / 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 / GPCR, family 3, metabotropic glutamate receptor / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / : / Arrestin (or S-antigen), N-terminal domain ...GPCR, family 3, metabotropic glutamate receptor 3 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / GPCR, family 3, metabotropic glutamate receptor / 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 / 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: 3.9 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 19, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60589.png

Downloads & links

-
Map

FileDownload / File: emd_60589.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-0.07263484 - 1.1102294
Average (Standard dev.)0.0036934083 (±0.018324299)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
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

-
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: 150 KDa

-
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

-
Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

-
Macromolecule #3: scFv30

MacromoleculeName: scFv30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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

-
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

-
Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE / Details: Ab-initio reconstruction by CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39446
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more