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- EMDB-68390: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-68390
TitleCryo-EM structure of the mGlu7-beta-arrestin 1 complex
Map data
Sample
  • Complex: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex
    • Protein or peptide: Isoform 4 of Metabotropic glutamate receptor 7
    • Protein or peptide: beta-arrestin 1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: CHOLESTEROL
KeywordsGPCR / Metabotropic glutamate receptor / beta-arrestin / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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 / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding / axon development ...negative regulation of glutamate secretion / group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / sensory perception of sound / adenylate cyclase inhibitor activity / dendritic shaft / PDZ domain binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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
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, 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 / 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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLin S / Zhang C / Wei J / Chen K / Feng Y / Wang Z / Chu X / Yi C / Ma L / Han S ...Lin S / Zhang C / Wei J / Chen K / Feng Y / Wang Z / Chu X / Yi C / Ma L / Han S / Zhao Q / Wu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32530052 China
National Science Foundation (NSF, China)82121005 China
CitationJournal: To be published
Title: Subtype-dependent arrestin engagement of the metabotropic glutamate receptors
Authors: Lin S / Zhang C / Wei J / Yu J / Li S / Xu J / Su J / Chen K / Feng Y / Wang Z / Chu X / Yi C / Ma L / Han S / Zhang H / Shui W / Zhao Q / Wu B
History
DepositionJan 14, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68390.png

Downloads & links

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Map

FileDownload / File: emd_68390.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.39534023 - 3.6051455
Average (Standard dev.)0.008419852 (±0.032888826)
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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Sample components

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Entire : Cryo-EM structure of the mGlu7-beta-arrestin 1 complex

EntireName: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex
Components
  • Complex: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex
    • Protein or peptide: Isoform 4 of Metabotropic glutamate receptor 7
    • Protein or peptide: beta-arrestin 1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: CHOLESTEROL

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Supramolecule #1: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex

SupramoleculeName: Cryo-EM structure of the mGlu7-beta-arrestin 1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 4 of Metabotropic glutamate receptor 7

MacromoleculeName: Isoform 4 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: 102.004625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDGSW SHPQFEKGSG SWSHPQFEKG SSENLYFQSQ EMYAPHSIRI EGDVTLGGLF PVHAKGPSGV PCGDIKRENG IHRLEAMLY ALDQINSDPN LLPNVTLGAR ILDTCSRDTY ALEQSLTFVQ ALIQKDTSDV RCTNGEPPVF VKPEKVVGVI G ASGSSVSI ...String:
DYKDDDDGSW SHPQFEKGSG SWSHPQFEKG SSENLYFQSQ EMYAPHSIRI EGDVTLGGLF PVHAKGPSGV PCGDIKRENG IHRLEAMLY ALDQINSDPN LLPNVTLGAR ILDTCSRDTY ALEQSLTFVQ ALIQKDTSDV RCTNGEPPVF VKPEKVVGVI G ASGSSVSI MVANILRLFQ IPQISYASTA PELSDDRRYD FFSRVVPPDS FQAQAMVDIV KALGWNYVST LASEGSYGEK GV ESFTQIS KEAGGLCIAQ SVRIPQERKD RTIDFDRIIK QLLDTPNSRA VVIFANDEDI KQILAAAKRA DQVGHFLWVG SDS WGSKIN PLHQHEDIAE GAITIQPKRA TVEGFDAYFT SRTLENNRRN VWFAEYWEEN FNCKLTISGS KKEDTDRKCT GQER IGKDS NYEQEGKVQF VIDAVYAMAH ALHHMNKDLC ADYRGVCPEM EQAGGKKLLK YIRNVNFNGS AGTPVMFNKN GDAPG RYDI FQYQTTNTSN PGYRLIGQWT DELQLNIEDM QWGKGVREIP ASVCTLPCKP GQRKKTQKGT PCCWTCEPCD GYQYQF DEM TCQHCPYDQR PNENRTGCQD IPIIKLEWHS PWAVIPVFLA MLGIIATIFV MATFIRYNDT PIVRASGREL SYVLLTG IF LCYIITFLMI AKPDVAVCSF RRVFLGLGMC ISYAALLTKT NRIYRIFEQG KKSVTAPRLI SPTSQLAITS SLISVQLL G VFIWFGVDPP NIIIDYDEHK TMNPEQARGV LKCDITDLQI ICSLGYSILL MVTCTVYAIK TRGVPENFNE AKPIGFTMY TTCIVWLAFI PIFFGTAQSA EKLYIQTTTL TISMNLSASV ALGMLYMPKV YIIIFHPELN VQKRKRSFKA VVTAATMSSR ARGRTPPSL GPQDESC(TPO)(TPO)A (SEP)(SEP)(SEP)LAKDTSS

UniProtKB: Metabotropic glutamate receptor 7

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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: 56.556043 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL EVQLVESGGG LVQPGGSLRL SCAA SGFNV YSSSIHWVRQ APGKGLEWVA SISSYYGYTY YADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARS RQFWY SGLD YWGQGTLVTV SSAHHHHHHH H

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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: 11.976338 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TT

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Macromolecule #4: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 4 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 5 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7epc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 679074
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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