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- EMDB-48111: Human M5 muscarinic acetylcholine receptor complex with mini-Gq a... -

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Entry
Database: EMDB / ID: EMD-48111
TitleHuman M5 muscarinic acetylcholine receptor complex with mini-Gq and iperoxo
Map dataHuman M5 muscarinic acetylcholine receptor complex with mini-Gq and iperoxo
Sample
  • Complex: Human M5-miniGq-Gb1g2 complex
    • Protein or peptide: Muscarinic acetylcholine receptor M5
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein Gq alpha subunit chimera
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
KeywordsG protein-coupled receptor / acetylcholine binding / seven transmembrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of phosphatidylinositol dephosphorylation / gastric acid secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / G protein-coupled serotonin receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / dopamine transport / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / G-protein activation / Activation of the phototransduction cascade ...regulation of phosphatidylinositol dephosphorylation / gastric acid secretion / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / G protein-coupled serotonin receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / dopamine transport / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / photoreceptor outer segment membrane / spectrin binding / alkylglycerophosphoethanolamine phosphodiesterase activity / transmission of nerve impulse / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / photoreceptor outer segment / cardiac muscle cell apoptotic process / photoreceptor inner segment / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / cell body / positive regulation of cytosolic calcium ion concentration / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / cellular response to hypoxia / chemical synaptic transmission / postsynaptic membrane / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / protein-containing complex binding / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
Muscarinic acetylcholine receptor M5 / Muscarinic acetylcholine receptor family / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein ...Muscarinic acetylcholine receptor M5 / Muscarinic acetylcholine receptor family / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Muscarinic acetylcholine receptor M5 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsBurger WAC / Mobbs JI / Thal DM
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1196951 Australia
Australian Research Council (ARC)LP180100560 Australia
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM reveals an extrahelical allosteric binding site at the M mAChR.
Authors: Wessel A C Burger / Jesse I Mobbs / Bhavika Rana / Jinan Wang / Keya Joshi / Patrick R Gentry / Mahmuda Yeasmin / Hariprasad Venugopal / Aaron M Bender / Craig W Lindsley / Yinglong Miao / ...Authors: Wessel A C Burger / Jesse I Mobbs / Bhavika Rana / Jinan Wang / Keya Joshi / Patrick R Gentry / Mahmuda Yeasmin / Hariprasad Venugopal / Aaron M Bender / Craig W Lindsley / Yinglong Miao / Arthur Christopoulos / Celine Valant / David M Thal /
Abstract: The M muscarinic acetylcholine receptor (M mAChR) represents a promising therapeutic target for neurological disorders. However, the high conservation of its orthosteric binding site poses ...The M muscarinic acetylcholine receptor (M mAChR) represents a promising therapeutic target for neurological disorders. However, the high conservation of its orthosteric binding site poses significant challenges for drug development. While selective positive allosteric modulators (PAMs) offer a potential solution, a structural understanding of the M mAChR and its allosteric binding sites remains limited. Here, we present a 2.8 Å cryo-electron microscopy structure of the M mAChR complexed with heterotrimeric G protein and the agonist iperoxo, completing the active-state structural characterization of the mAChR family. To identify the binding site of M-selective PAMs, we implement an integrated approach combining mutagenesis, pharmacological assays, structural biology, and molecular dynamics simulations. Our mutagenesis studies reveal that selective M PAMs bind outside previously characterized M mAChR allosteric sites. Subsequently, we obtain a 2.1 Å structure of M mAChR co-bound with acetylcholine and the selective PAM VU6007678, revealing an allosteric pocket at the extrahelical interface between transmembrane domains 3 and 4 that is confirmed through mutagenesis and simulations. These findings demonstrate the diverse mechanisms of allosteric regulation in mAChRs and highlight the value of integrating pharmacological and structural approaches to identify allosteric binding sites.
History
DepositionNov 30, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48111.png

Downloads & links

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Map

FileDownload / File: emd_48111.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman M5 muscarinic acetylcholine receptor complex with mini-Gq and iperoxo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.37814048 - 1.1742731
Average (Standard dev.)0.006791838 (±0.038462676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 195.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48111_msk_1.map
Projections & Slices
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Half map: Half Map B

Fileemd_48111_half_map_1.map
AnnotationHalf Map B
Projections & Slices
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Histogram (log scale)

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Half map: Half Map A

Fileemd_48111_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : Human M5-miniGq-Gb1g2 complex

EntireName: Human M5-miniGq-Gb1g2 complex
Components
  • Complex: Human M5-miniGq-Gb1g2 complex
    • Protein or peptide: Muscarinic acetylcholine receptor M5
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein Gq alpha subunit chimera
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium

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Supramolecule #1: Human M5-miniGq-Gb1g2 complex

SupramoleculeName: Human M5-miniGq-Gb1g2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Muscarinic acetylcholine receptor M5

MacromoleculeName: Muscarinic acetylcholine receptor M5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.190051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAEG DSYHNATTVN GTPVNHQPLE RHRLWEVITI AAVTAVVSLI TIVGNVLVMI SFKVNSQLKT VNNYYLLSLA CADLIIGIF SMNLYTTYIL MGRWALGSLA CDLWLALDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR TPKRAGIMIG L AWLISFIL ...String:
DYKDDDDAEG DSYHNATTVN GTPVNHQPLE RHRLWEVITI AAVTAVVSLI TIVGNVLVMI SFKVNSQLKT VNNYYLLSLA CADLIIGIF SMNLYTTYIL MGRWALGSLA CDLWLALDYV ASNASVMNLL VISFDRYFSI TRPLTYRAKR TPKRAGIMIG L AWLISFIL WAPAILCWQY LVGKRTVPLD ECQIQFLSEP TITFGTAIAA FYIPVSVMTI LYCRIYRETE KRTKDLADLQ GS DSVPSHQ MTKRKRVVLV KERKAAQTLS AILLAFIITW TPYNIMVLVS TFCDKCVPVT LWHLGYWLCY VNSTVNPICY ALC NRTFRK TFKMLLLCRW KKKKVEE

UniProtKB: Muscarinic acetylcholine receptor M5, Muscarinic acetylcholine receptor M5

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 38.534062 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV ...String:
MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD IN AICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAG HDNRVS CLGVTDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein Gq alpha subunit chimera

MacromoleculeName: Guanine nucleotide-binding protein Gq alpha subunit chimera
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.039793 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GCTLSAEDKA AVERSKMIDR NLREDGEKAR RTLRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIFE TKFQVDKVNF HMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR ...String:
GCTLSAEDKA AVERSKMIDR NLREDGEKAR RTLRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIFE TKFQVDKVNF HMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR YTTPEDATPE PGEDPRVTRA KYFIRKEFVD ISTASGDGRH ICYPHFTCAV DTENARRIFN DCKDIILQMN LR EYNLV

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.56375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #5: 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: 5 / 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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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 426714
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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