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- EMDB-30671: apo state of class C GPCR -

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Basic information

Entry
Database: EMDB / ID: EMD-30671
Titleapo state of class C GPCR
Map data
Sample
  • Cell: dimer of apo state
    • Protein or peptide: Metabotropic glutamate receptor 1
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / regulation of synaptic transmission, glutamatergic / sensory perception of pain / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Sensory perception of sweet, bitter, and umami (glutamate) taste / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / dendrite / glutamatergic synapse / nucleus / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 1 / 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 ...GPCR, family 3, metabotropic glutamate receptor 1 / 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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsZhang JY / Wu LJ / Luo F / Hua T / Liu ZJ
CitationJournal: Protein Cell / Year: 2021
Title: Structural insights into the activation initiation of full-length mGlu1.
Authors: Jinyi Zhang / Lu Qu / Lijie Wu / Xiaomeng Tang / Feng Luo / Weixiu Xu / Yueming Xu / Zhi-Jie Liu / Tian Hua /
History
DepositionNov 11, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dgd
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dgd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30671.png

Downloads & links

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Map

FileDownload / File: emd_30671.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.41 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.1
Minimum - Maximum-0.7673757 - 0.9251982
Average (Standard dev.)-0.0008372346 (±0.02229979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 304.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z304.560304.560304.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.7670.925-0.001

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Supplemental data

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Sample components

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Entire : dimer of apo state

EntireName: dimer of apo state
Components
  • Cell: dimer of apo state
    • Protein or peptide: Metabotropic glutamate receptor 1

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Supramolecule #1: dimer of apo state

SupramoleculeName: dimer of apo state / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Metabotropic glutamate receptor 1

MacromoleculeName: Metabotropic glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.300883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GASSQRSVAR MDGDVIIGAL FSVHHQPPAE KVPERKCGEI REQYGIQRVE AMFHTLDKIN ADPVLLPNIT LGSEIRDSCW HSSVALEQS IEFIRDSLIS IRDEKDGINR CLPDGQSLPP GRTKKPIAGV IGPGSSSVAI QVQNLLQLFD IPQIAYSATS I DLSDKTLY ...String:
GASSQRSVAR MDGDVIIGAL FSVHHQPPAE KVPERKCGEI REQYGIQRVE AMFHTLDKIN ADPVLLPNIT LGSEIRDSCW HSSVALEQS IEFIRDSLIS IRDEKDGINR CLPDGQSLPP GRTKKPIAGV IGPGSSSVAI QVQNLLQLFD IPQIAYSATS I DLSDKTLY KYFLRVVPSD TLQARAMLDI VKRYNWTYVS AVHTEGNYGE SGMDAFKELA AQEGLCIAHS DKIYSNAGEK SF DRLLRKL RERLPKARVV VCFCEGMTVR GLLSAMRRLG VVGEFSLIGS DGWADRDEVI EGYEVEANGG ITIKLQSPEV RSF DDYFLK LRLDTNTRNP WFPEFWQHRF QCRLPGHLLE NPNFKRICTG NESLEENYVQ DSKMGFVINA IYAMAHGLQN MHHA LCPGH VGLCDAMKPI DGSKLLDFLI KSSFIGVSGE EVWFDEKGDA PGRYDIMNLQ YTEANRYDYV HVGTWHEGVL NIDDY KIQM NKSGVVRSVC SEPCLKGQIK VIRKGEVSCC WICTACKENE YVQDEFTCKA CDLGWWPNAD LTGCEPIPVR YLEWSN IES IIAIAFSCLG ILVTLFVTLI FVLYRDTPVV KSSSRELCYI ILAGIFLGYV CPFTLIAKPT TTSCYLQRLL VGLSSAM CY SALVTKTNRI ARILAGSKKK ICTRKPRFMS AWAQVIIASI LISVQLTLVV TLIIMEPPMP ILSYPSIKEV YLICNTSN L GVVAPLGYNG LLIMSCTYYA FKTRNVPANF NEAKYIAFTM YTTCIIWLAF VPIYFGSNYK IITTCFAVSL SVTVALGCM FTPKMYIIIA KPERNVRSAF TTSDVVRMHV GDG

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.78 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134512

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