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- EMDB-32530: Cryo-EM structure of LY2794193-bound mGlu3 -

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Basic information

Entry
Database: EMDB / ID: EMD-32530
TitleCryo-EM structure of LY2794193-bound mGlu3
Map dataCryo-EM structure of LY2794193-bound mGlu3.
Sample
  • Complex: Cryo-EM structure of mGlu3 bound with LY2794193
    • Protein or peptide: Metabotropic glutamate receptor 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
KeywordsGlutamate / G protein-coupled receptor / Cryo-EM / Selective ligand / MEMBRANE PROTEIN
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity ...group II metabotropic glutamate receptor activity / negative regulation of adenylate cyclase activity / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / astrocyte projection / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity / G protein-coupled receptor activity / presynaptic membrane / scaffold protein binding / G alpha (i) signalling events / gene expression / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynaptic density / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / 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 3 / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsFang W / Yang F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21825703 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis of the activation of metabotropic glutamate receptor 3.
Authors: Wei Fang / Fan Yang / Chanjuan Xu / Shenglong Ling / Li Lin / Yingxin Zhou / Wenjing Sun / Xiaomei Wang / Peng Liu / Philippe Rondard / Pan Shi / Jean-Philippe Pin / Changlin Tian / Jianfeng Liu /
History
DepositionJan 3, 2022-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing 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 cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7wih
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32530.png

Downloads & links

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Map

FileDownload / File: emd_32530.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of LY2794193-bound mGlu3.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å		1.01 Å/pix.
x 320 pix.
= 324.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-1.2305377 - 1.3469175
Average (Standard dev.)0.00021664832 (±0.017955119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z324.480324.480324.480
α/β/γ90.00090.00090.000
start NX/NY/NZ139118109
NX/NY/NZ123164187
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.2311.3470.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of mGlu3 bound with LY2794193

EntireName: Cryo-EM structure of mGlu3 bound with LY2794193
Components
  • Complex: Cryo-EM structure of mGlu3 bound with LY2794193
    • Protein or peptide: Metabotropic glutamate receptor 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid

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Supramolecule #1: Cryo-EM structure of mGlu3 bound with LY2794193

SupramoleculeName: Cryo-EM structure of mGlu3 bound with LY2794193 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Metabotropic glutamate receptor 3

MacromoleculeName: Metabotropic glutamate receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.021695 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDENLYFQG LGDHNFLRRE IKIEGDLVLG GLFPINEKGT GTEECGRINE DRGIQRLEAM LFAIDEINK DDYLLPGVKL GVHILDTCSR DTYALEQSLE FVRASLTKVD EAEYMCPDGS YAIQENIPLL IAGVIGGSYS S VSIQVANL ...String:
MKTIIALSYI FCLVFADYKD DDDENLYFQG LGDHNFLRRE IKIEGDLVLG GLFPINEKGT GTEECGRINE DRGIQRLEAM LFAIDEINK DDYLLPGVKL GVHILDTCSR DTYALEQSLE FVRASLTKVD EAEYMCPDGS YAIQENIPLL IAGVIGGSYS S VSIQVANL LRLFQIPQIS YASTSAKLSD KSRYDYFART VPPDFYQAKA MAEILRFFNW TYVSTVASEG DYGETGIEAF EQ EARLRNI CIATAEKVGR SNIRKSYDSV IRELLQKPNA RVVVLFMRSD DSRELIAAAS RANASFTWVA SDGWGAQESI IKG SEHVAY GAITLELASQ PVRQFDRYFQ SLNPYNNHRN PWFRDFWEQK FQCSLQNKRN HRRVCDKHLA IDSSNYEQES KIMF VVNAV YAMAHALHKM QRTLCPNTTK LCDAMKILDG KKLYKDYLLK INFTAPFNPN KDADSIVKFD TFGDGMGRYN VFNFQ NVGG KYSYLKVGHW AETLSLDVNS IHWSRNSVPT SQCSDPCAPN EMKNMQPGDV CCWICIPCEP YEYLADEFTC MDCGSG QWP TADLTGCYDL PEDYIRWEDA WAIGPVTIAC LGFMCTCMVV TVFIKHNNTP LVKASGRELC YILLFGVGLS YCMTFFF IA KPSPVICALR RLGLGSSFAI CYSALLTKTN CIARIFDGVK NGAQRPKFIS PSSQVFICLG LILVQIVMVS VWLILEAP G TRRYTLAEKR ETVILKCNVK DSSMLISLTY DVILVILCTV YAFKTRKCPE NFNEAKFIGF TMYTTCIIWL AFLPIFYVT SSDYRVQTTT MCISVSLSGF VVLGCLFAPK VHIILFQPQK NVVTHRLHLN RFSVSGTGTT YSQSSASTYV PTVCNGREVL DSTTSSL

UniProtKB: Metabotropic glutamate receptor 3

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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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Macromolecule #3: (1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bi...

MacromoleculeName: (1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
type: ligand / ID: 3 / Number of copies: 2 / Formula: CWY
Molecular weightTheoretical: 334.324 Da
Chemical component information

ChemComp-CWY:
(1S,2S,4S,5R,6S)-2-amino-4-[(3-methoxybenzene-1-carbonyl)amino]bicyclo[3.1.0]hexane-2,6-dicarboxylic acid

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6n51

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288762
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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