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- EMDB-41069: CDPPB-bound inactive mGlu5 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41069
TitleCDPPB-bound inactive mGlu5
Map data
Sample
  • Organelle or cellular component: Metabotropic glutamate receptor 5 in complex with CDPPB
    • Protein or peptide: Metabotropic glutamate receptor 5
  • Ligand: 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide
KeywordsGPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) ...A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / dendritic shaft / protein tyrosine kinase binding / learning / locomotory behavior / synapse organization / postsynaptic density membrane / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / chemical synaptic transmission / G alpha (q) signalling events / dendritic spine / learning or memory / positive regulation of MAPK cascade / neuronal cell body / dendrite / regulation of DNA-templated transcription / 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 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily ...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 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
Similarity search - Domain/homology
Metabotropic glutamate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKrishna Kumar K / Wang H / Kobilka BK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS028471 United States
CitationJournal: bioRxiv / Year: 2023
Title: Step-wise activation of a Family C GPCR.
Authors: Kaavya Krishna Kumar / Haoqing Wang / Chris Habrian / Naomi R Latorraca / Jun Xu / Evan S O'Brien / Chensong Zhang / Elizabeth Montabana / Antoine Koehl / Susan Marqusee / Ehud Y Isacoff / Brian K Kobilka /
Abstract: Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain (ECD) that is linked via a cysteine- ...Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain (ECD) that is linked via a cysteine-rich domain (CRDs) to their 7-transmembrane (TM) domain. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the ECD to the G protein-coupling TM. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging we reveal distinct receptor conformations upon allosteric modulator and G protein binding.
History
DepositionJun 16, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41069.png

Downloads & links

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Map

FileDownload / File: emd_41069.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 360 pix.
= 306.756 Å		0.85 Å/pix.
x 360 pix.
= 306.756 Å		0.85 Å/pix.
x 360 pix.
= 306.756 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.57
Minimum - Maximum-19.216154 - 96.651430000000005
Average (Standard dev.)0.000000000002173 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.756 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Metabotropic glutamate receptor 5 in complex with CDPPB

EntireName: Metabotropic glutamate receptor 5 in complex with CDPPB
Components
  • Organelle or cellular component: Metabotropic glutamate receptor 5 in complex with CDPPB
    • Protein or peptide: Metabotropic glutamate receptor 5
  • Ligand: 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide

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Supramolecule #1: Metabotropic glutamate receptor 5 in complex with CDPPB

SupramoleculeName: Metabotropic glutamate receptor 5 in complex with CDPPB
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 98.868297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAAQSSER RVVAHMPGDI IIGALFSVHH QPTVDKVHER KCGAVREQYG IQRVEAMLHT LERINSDPT LLPNITLGCE IRDSCWHSAV ALEQSIEFIR DSLISSEEEE GLVRCVDGSS SSFRSKKPIV GVIGPGSSSV A IQVQNLLQ ...String:
MKTIIALSYI FCLVFADYKD DDDAAQSSER RVVAHMPGDI IIGALFSVHH QPTVDKVHER KCGAVREQYG IQRVEAMLHT LERINSDPT LLPNITLGCE IRDSCWHSAV ALEQSIEFIR DSLISSEEEE GLVRCVDGSS SSFRSKKPIV GVIGPGSSSV A IQVQNLLQ LFNIPQIAYS ATSMDLSDKT LFKYFMRVVP SDAQQARAMV DIVKRYNWTY VSAVHTEGNY GESGMEAFKD MS AKEGICI AHSYKIYSNA GEQSFDKLLK KLTSHLPKAR VVACFCEGMT VRGLLMAMRR LGLAGEFLLL GSDGWADRYD VTD GYQREA VGGITIKLQS PDVKWFDDYY LKLRPETNHR NPWFQEFWQH RFQCRLEGFP QENSKYNKTC NSSLTLKTHH VQDS KMGFV INAIYSMAYG LHNMQMSLCP GYAGLCDAMK PIDGRKLLES LMKTNFTGVS GDTILFDENG DSPGRYEIMN FKEMG KDYF DYINVGSWDN GELKMDDDEV WSKKSNIIRS VCSEPCEKGQ IKVIRKGEVS CCWTCTPCKE NEYVFDEYTC KACQLG SWP TDDLTGCDLI PVQYLRWGDP EPIAAVVFAC LGLLATLFVT VVFIIYRDTP VVKSSSRELC YIILAGICLG YLCTFCL IA KPKQIYCYLQ RIGIGLSPAM SYSALVTKTN RIARILAGSK KKICTKKPRF MSACAQLVIA FILICIQLGI IVALFIME P PDIMHDYPSI REVYLICNTT NLGVVTPLGY NGLLILSCTF YAFKTRNVPA NFNEAKYIAF TMYTTCIIWL AFVPIYFGS NYKIITMCFS VSLSATVALG CMFVPKVYII LAKPERNVRS AFTTSTVVRM HVGDGKSSSA ASRSSSLVNL WKRRGSSGET L

UniProtKB: Metabotropic glutamate receptor 5

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Macromolecule #2: 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide

MacromoleculeName: 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide / type: ligand / ID: 2 / Number of copies: 2 / Formula: YKU
Molecular weightTheoretical: 364.399 Da
Chemical component information

ChemComp-YKU:
3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide

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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: 7.4
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: 52.2 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: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

0346

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246232
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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