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- EMDB-63988: cryo-EM structure of ligand-free active-state M1 muscarinic acety... -

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Basic information

Entry
Database: EMDB / ID: EMD-63988
Titlecryo-EM structure of ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex
Map data
Sample
  • Complex: Ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex/de novo design fusion protein
    • Protein or peptide: M1 muscarinic acetylcholine receptor, de novo design protein
    • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-11
KeywordsGPCR / active-state / ligand-free / de novo protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of melanocyte differentiation / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / developmental pigmentation / cellular response to pH / PLC beta mediated events / entrainment of circadian clock ...regulation of melanocyte differentiation / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Acetylcholine regulates insulin secretion / endothelin receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / developmental pigmentation / cellular response to pH / PLC beta mediated events / entrainment of circadian clock / cranial skeletal system development / ligand-gated ion channel signaling pathway / action potential / phototransduction, visible light / photoreceptor outer segment / enzyme regulator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / skeletal system development / G protein-coupled receptor binding / positive regulation of insulin secretion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / ADP signalling through P2Y purinoceptor 1 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / heterotrimeric G-protein complex / Thrombin signalling through proteinase activated receptors (PARs) / heart development / G protein activity / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / lysosomal membrane / GTPase activity / synapse / GTP binding / signal transduction / extracellular exosome / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
G-protein alpha subunit, group Q / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit alpha-11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsZhang X / Gao K / Liu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122041 China
CitationJournal: To Be Published
Title: cryo-EM structure of ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex
Authors: Zhang X / Gao K / Liu X
History
DepositionApr 1, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63988.png

Downloads & links

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Map

FileDownload / File: emd_63988.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.607326 - 3.0874395
Average (Standard dev.)-0.0003644062 (±0.046833407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63988_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_63988_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63988_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Ligand-free active-state M1 muscarinic acetylcholine receptor wit...

EntireName: Ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex/de novo design fusion protein
Components
  • Complex: Ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex/de novo design fusion protein
    • Protein or peptide: M1 muscarinic acetylcholine receptor, de novo design protein
    • Protein or peptide: Guanine nucleotide-binding protein subunit alpha-11

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Supramolecule #1: Ligand-free active-state M1 muscarinic acetylcholine receptor wit...

SupramoleculeName: Ligand-free active-state M1 muscarinic acetylcholine receptor with alpha5 helix of G11 protein complex/de novo design fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: M1 muscarinic acetylcholine receptor, de novo design protein

MacromoleculeName: M1 muscarinic acetylcholine receptor, de novo design protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.07073 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VAFIGITTGL LSLATVTGNL LVLISFKVNT ELKTVNNYFL LSLACADLII GTFSMNLYTT YLLMGHWALG TLACDLWLAL DYVASNASV MNLLLISFDR YFSVTRPLSY RAKRTPRRAA LMIGLAWLVS FVLWAPAILF WQYLVGERTV LAGQCYIQFL S QPIITFGT ...String:
VAFIGITTGL LSLATVTGNL LVLISFKVNT ELKTVNNYFL LSLACADLII GTFSMNLYTT YLLMGHWALG TLACDLWLAL DYVASNASV MNLLLISFDR YFSVTRPLSY RAKRTPRRAA LMIGLAWLVS FVLWAPAILF WQYLVGERTV LAGQCYIQFL S QPIITFGT AMAAFYLPVT VMCTLYWRIY RETKRAGERL AKLLEKFEAL PLEDIVAALK ALLATNRPEI QLAVKTIVEN FP EIKKEAE KLTPEQKAKL AALEAQLADL PEELRKVLLS MYLTGLLYGG SEENRKRAIE KAARTLSAIL LAFILTWTPY NIM VLVSTF CKDCVPETLW ELGYWLCYVN STINPMCYAL CNKAFRDTFR LLLLCR

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Macromolecule #2: Guanine nucleotide-binding protein subunit alpha-11

MacromoleculeName: Guanine nucleotide-binding protein subunit alpha-11 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.15266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
TPENIRFVFA AVKDTILQLN LKEYNLV

UniProtKB: Guanine nucleotide-binding protein subunit alpha-11

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 155176
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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