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- EMDB-27970: CryoEM structure of miniGq-coupled hM3R in complex with iperoxo (... -

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Basic information

Entry
Database: EMDB / ID: EMD-27970
TitleCryoEM structure of miniGq-coupled hM3R in complex with iperoxo (local refinement)
Map dataCryoEM structure of Gq-coupled hM3R in complex with Iperoxo
Sample
  • Complex: hM3R
    • Protein or peptide: Muscarinic acetylcholine receptor M3
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsGPCR / IXO / active state / MEMBRANE PROTEIN / hM3R / Iperoxo
Function / homology
Function and homology information


saliva secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / Acetylcholine regulates insulin secretion / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / positive regulation of smooth muscle contraction / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / acetylcholine binding ...saliva secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / Acetylcholine regulates insulin secretion / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / positive regulation of smooth muscle contraction / regulation of smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / acetylcholine binding / acetylcholine receptor signaling pathway / ligand-gated ion channel signaling pathway / smooth muscle contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / basal plasma membrane / calcium-mediated signaling / positive regulation of insulin secretion / protein modification process / G protein-coupled acetylcholine receptor signaling pathway / nervous system development / signaling receptor activity / basolateral plasma membrane / G alpha (q) signalling events / chemical synaptic transmission / postsynaptic membrane / G protein-coupled receptor signaling pathway / synapse / dendrite / endoplasmic reticulum membrane / signal transduction / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M3 / Muscarinic acetylcholine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Muscarinic acetylcholine receptor M3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsZhang S / Fay JF / Roth BL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH112205 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U24DK1169195 United States
CitationJournal: Nature / Year: 2022
Title: Molecular basis for selective activation of DREADD-based chemogenetics.
Authors: Shicheng Zhang / Ryan H Gumpper / Xi-Ping Huang / Yongfeng Liu / Brian E Krumm / Can Cao / Jonathan F Fay / Bryan L Roth /
Abstract: Designer receptors exclusively activated by designer drugs (DREADDs) represent a powerful chemogenetic technology for the remote control of neuronal activity and cellular signalling. The muscarinic ...Designer receptors exclusively activated by designer drugs (DREADDs) represent a powerful chemogenetic technology for the remote control of neuronal activity and cellular signalling. The muscarinic receptor-based DREADDs are the most widely used chemogenetic tools in neuroscience research. The G-coupled DREADD (hM3Dq) is used to enhance neuronal activity, whereas the G-coupled DREADD (hM4Di) is utilized to inhibit neuronal activity. Here we report four DREADD-related cryogenic electron microscopy high-resolution structures: a hM3Dq-miniG complex and a hM4Di-miniG complex bound to deschloroclozapine; a hM3Dq-miniG complex bound to clozapine-N-oxide; and a hM3R-miniG complex bound to iperoxo. Complemented with mutagenesis, functional and computational simulation data, our structures reveal key details of the recognition of DREADD chemogenetic actuators and the molecular basis for activation. These findings should accelerate the structure-guided discovery of next-generation chemogenetic tools.
History
DepositionAug 27, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27970.png

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Map

FileDownload / File: emd_27970.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of Gq-coupled hM3R in complex with Iperoxo
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 288 pix.
= 253.44 Å		0.88 Å/pix.
x 288 pix.
= 253.44 Å		0.88 Å/pix.
x 288 pix.
= 253.44 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.08661633 - 2.6630952
Average (Standard dev.)-0.000054930457 (±0.014722539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27970_msk_1.map
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Additional map: Additional Map

Fileemd_27970_additional_1.map
AnnotationAdditional Map
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Half map: Half Map 1

Fileemd_27970_half_map_1.map
AnnotationHalf Map 1
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Half map: Half Map 2

Fileemd_27970_half_map_2.map
AnnotationHalf Map 2
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Sample components

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Entire : hM3R

EntireName: hM3R
Components
  • Complex: hM3R
    • Protein or peptide: Muscarinic acetylcholine receptor M3
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: hM3R

SupramoleculeName: hM3R / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Muscarinic acetylcholine receptor M3

MacromoleculeName: Muscarinic acetylcholine receptor M3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.966617 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AGNFSSPDGT TDDPLGGHTV WQVVFIAFLT GILALVTIIG NILVIVSFKV NKQLKTVNNY FLLSLACADL IIGVISMNLF TTYIIMNRW ALGNLACDLW LAIDYVASNA SVMNLLVISF DRYFSITRPL TYRAKRTTKR AGVMIGLAWV ISFVLWAPAI L FWQYFVGK ...String:
AGNFSSPDGT TDDPLGGHTV WQVVFIAFLT GILALVTIIG NILVIVSFKV NKQLKTVNNY FLLSLACADL IIGVISMNLF TTYIIMNRW ALGNLACDLW LAIDYVASNA SVMNLLVISF DRYFSITRPL TYRAKRTTKR AGVMIGLAWV ISFVLWAPAI L FWQYFVGK RTVPPGECFI QFLSEPTITF GTAIAAFYMP VTIMTILYWR IYKETEKRTK ELAGLQASGT EAETENFVHP AK RFALKTR SQITKRKRMS LVKEKKAAQT LSAILLAFII TWTPYNIMVL VNTFCDSCIP KTFWNLGYWL CYINSTVNPV CYA LCNKTF RTTFKMLLLC QCDKKKRRKQ QYQQRQSVIF HKRAPEQALG GSGGGGSGGS SSGGGGSGGG GSGGSSSGGV FTLE DFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIEEVFKV VYPVD DHHF KVILPYGTLV IDGVTPNMLN YFGRPYEGIA VFDGKKITVT GTLWNGNKII DERLITPDGS MLFRVTINSG GSGGHH HHH HHHHH

UniProtKB: Muscarinic acetylcholine receptor M3, Muscarinic acetylcholine receptor M3

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Macromolecule #2: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium

MacromoleculeName: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
type: ligand / ID: 2 / Number of copies: 1 / Formula: IXO
Molecular weightTheoretical: 197.254 Da
Chemical component information

ChemComp-IXO:
4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2858 / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6oij

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 591814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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