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- EMDB-30672: intermediate state of class C GPCR -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-30672
Titleintermediate state of class C GPCR
Map data
Sample
  • Cell: dimer of intermediate state
    • Protein or peptide: Metabotropic glutamate receptor 1
    • Protein or peptide: nanobody
  • Ligand: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
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 / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / regulation of sensory perception of pain / 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 / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / regulation of sensory perception of pain / L-glutamate import across plasma membrane / G protein-coupled glutamate receptor signaling pathway / 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 / glutamatergic synapse / dendrite / 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 ...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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dge
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dge
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30672.png

Downloads & links

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Map

FileDownload / File: emd_30672.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 288 pix.
= 299.52 Å		1.04 Å/pix.
x 288 pix.
= 299.52 Å		1.04 Å/pix.
x 288 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.015
Minimum - Maximum-0.067678906 - 0.12244306
Average (Standard dev.)0.00017904979 (±0.0021431788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 299.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z299.520299.520299.520
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/NS288288288
D min/max/mean-0.0680.1220.000

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Supplemental data

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Sample components

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Entire : dimer of intermediate state

EntireName: dimer of intermediate state
Components
  • Cell: dimer of intermediate state
    • Protein or peptide: Metabotropic glutamate receptor 1
    • Protein or peptide: nanobody
  • Ligand: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID

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Supramolecule #1: dimer of intermediate state

SupramoleculeName: dimer of intermediate state / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 93.398867 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 LRLDTNHRNP WFQEFWQHRF QCRLEGFPQE NSNFKRICTG 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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Macromolecule #2: nanobody

MacromoleculeName: nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.354672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGRTFT SYAMGWFRQA PGKERESVAA ISSSGGSTHY ADSVKGRFTI SRDNSKNTVY LQMNSLKPE DTAVYYCAAA MYGSRWPDWE YDYWGQGTQV TVSS

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Macromolecule #3: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID

MacromoleculeName: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
type: ligand / ID: 3 / Number of copies: 1 / Formula: QUS
Molecular weightTheoretical: 189.126 Da
Chemical component information

ChemComp-QUS:
(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID / agonist*YM

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.33 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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