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- EMDB-68388: Cryo-EM structure of the mGlu5-beta-arrestin 1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-68388
TitleCryo-EM structure of the mGlu5-beta-arrestin 1 complex
Map data
Sample
  • Complex: mGlu5-beta-arrestin 1 complex
    • Protein or peptide: Metabotropic glutamate receptor 5
    • Protein or peptide: beta-arrestin 1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGPCR / Metabotropic glutamate receptor / beta-arrestin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


A2A adenosine receptor binding / sensory perception of hot stimulus / negative regulation of dendritic spine morphogenesis / : / operant conditioning / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / protein localization to nuclear inner membrane / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of cellular response to hypoxia ...A2A adenosine receptor binding / sensory perception of hot stimulus / negative regulation of dendritic spine morphogenesis / : / operant conditioning / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / protein localization to nuclear inner membrane / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of cellular response to hypoxia / positive regulation of long-term neuronal synaptic plasticity / positive regulation of sensory perception of pain / positive regulation of dopamine secretion / negative regulation of excitatory postsynaptic potential / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / positive regulation of neural precursor cell proliferation / Class C/3 (Metabotropic glutamate/pheromone receptors) / nuclear inner membrane / Neurexins and neuroligins / glutamate receptor activity / astrocyte projection / response to corticosterone / response to morphine / temperature homeostasis / protein tyrosine kinase activator activity / conditioned place preference / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / regulation of long-term synaptic depression / response to amphetamine / protein tyrosine kinase binding / dendritic shaft / synapse organization / postsynaptic density membrane / cognition / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / G protein-coupled receptor activity / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / response to ethanol / dendritic spine / G alpha (q) signalling events / positive regulation of MAPK cascade / learning or memory / response to antibiotic / neuronal cell body / regulation of DNA-templated transcription / dendrite / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_68388.png

Downloads & links

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Map

FileDownload / File: emd_68388.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 504 pix.
= 415.296 Å		0.82 Å/pix.
x 504 pix.
= 415.296 Å		0.82 Å/pix.
x 504 pix.
= 415.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.06759643 - 1.780975
Average (Standard dev.)0.00803263 (±0.024822535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 415.296 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : mGlu5-beta-arrestin 1 complex

EntireName: mGlu5-beta-arrestin 1 complex
Components
  • Complex: mGlu5-beta-arrestin 1 complex
    • Protein or peptide: Metabotropic glutamate receptor 5
    • Protein or peptide: beta-arrestin 1
    • Protein or peptide: scFv30
  • Ligand: GLUTAMIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mGlu5-beta-arrestin 1 complex

SupramoleculeName: mGlu5-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: Metabotropic glutamate receptor 5

MacromoleculeName: Metabotropic glutamate receptor 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.124969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSWSHPQFEK GSGAGASAGS WSHPQFEKGS DYKDDDDKEF LEVLFQGPSS ERRVVAHMPG DIIIGALFSV HHQPTVDKVH ERKCGAVRE QYGIQRVEAM LHTLERINSD PTLLPNITLG CEIRDSCWHS AVALEQSIEF IRDSLISSEE EEGLVRCVDG S SSSFRSKK ...String:
GSWSHPQFEK GSGAGASAGS WSHPQFEKGS DYKDDDDKEF LEVLFQGPSS ERRVVAHMPG DIIIGALFSV HHQPTVDKVH ERKCGAVRE QYGIQRVEAM LHTLERINSD PTLLPNITLG CEIRDSCWHS AVALEQSIEF IRDSLISSEE EEGLVRCVDG S SSSFRSKK PIVGVIGPGS SSVAIQVQNL LQLFNIPQIA YSATSMDLSD KTLFKYFMRV VPSDAQQARA MVDIVKRYNW TY VSAVHTE GNYGESGMEA FKDMSAKEGI CIAHSYKIYS NAGEQSFDKL LKKLTSHLPK ARVVACFCEG MTVRGLLMAM RRL GLAGEF LLLGSDGWAD RYDVTDGYQR EAVGGITIKL QSPDVKWFDD YYLKLRPETN HRNPWFQEFW QHRFQCRLEG FPQE NSKYN KTCNSSLTLK THHVQDSKMG FVINAIYSMA YGLHNMQMSL CPGYAGLCDA MKPIDGRKLL ESLMKTNFTG VSGDT ILFD ENGDSPGRYE IMNFKEMGKD YFDYINVGSW DNGELKMDDD EVWSKKSNII RSVCSEPCEK GQIKVIRKGE VSCCWT CTP CKENEYVFDE YTCKACQLGS WPTDDLTGCD LIPVQYLRWG DPEPIAAVVF ACLGLLATLF VTVVFIIYRD TPVVKSS SR ELCYIILAGI CLGYLCTFCL IAKPKQIYCY LQRIGIGLSP AMSYSALVTK TNRIARILAG SKKKICTKKP RFMSACAQ L VIAFILICIQ LGIIVALFIM EPPDIMHDYP SIREVYLICN TTNLGVVTPL GYNGLLILSC TFYAFKTRNV PANFNEAKY IAFTMYTTCI IWLAFVPIYF GSNYKIITMC FSVSLSATVA LGCMFVPKVY IILAKPERNV RSAF(TPO)T(SEP)(TPO) V VRMHVGDGKS SSAASRSSSL VNL

UniProtKB: Metabotropic glutamate receptor 5

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Macromolecule #2: beta-arrestin 1

MacromoleculeName: beta-arrestin 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.499957 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF 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 VFEDFAREVQ LVES GGGLV QPGGSLRLSC AASGFNVYSS SIHWVRQAPG KGLEWVASIS SYYGYTYYAD SVKGRFTISA DTSKNTAYLQ MNSLR AEDT AVYYCARSRQ FWYSGLDYWG QGTLVTVSSA HHHHHHHH

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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: 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: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: 2.0 µm / Nominal defocus min: 1.0 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:

6n51

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 312647
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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