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- EMDB-61411: cryo-EM structure of M1 muscarinic acetylcholine receptor in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-61411
Titlecryo-EM structure of M1 muscarinic acetylcholine receptor in complex with atropine
Map data
Sample
  • Complex: M1 muscarinic acetylcholine receptor/de novo design fusion protein
    • Protein or peptide: Muscarinic acetylcholine receptor M1,de novo design protein
  • Ligand: [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-2-phenyl-propanoate
KeywordsGPCR / inactive-state / de novo protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport / neuromuscular synaptic transmission ...saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport / neuromuscular synaptic transmission / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / regulation of locomotion / regulation of postsynaptic membrane potential / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / postsynaptic modulation of chemical synaptic transmission / axon terminus / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / G protein-coupled acetylcholine receptor signaling pathway / nervous system development / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / synapse / dendrite / glutamatergic synapse / signal transduction / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / 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 M1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao K / Zhang X / Liu X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974236 China
CitationJournal: To Be Published
Title: cryo-EM structure of M1 muscarinic acetylcholine receptor in complex with atropine
Authors: Gao K / Zhang X
History
DepositionSep 2, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61411.png

Downloads & links

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Map

FileDownload / File: emd_61411.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.)
0.84 Å/pix.
x 256 pix.
= 215.885 Å		0.84 Å/pix.
x 256 pix.
= 215.885 Å		0.84 Å/pix.
x 256 pix.
= 215.885 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.6381705 - 4.7969112
Average (Standard dev.)0.00048184732 (±0.06969134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.8848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61411_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61411_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : M1 muscarinic acetylcholine receptor/de novo design fusion protein

EntireName: M1 muscarinic acetylcholine receptor/de novo design fusion protein
Components
  • Complex: M1 muscarinic acetylcholine receptor/de novo design fusion protein
    • Protein or peptide: Muscarinic acetylcholine receptor M1,de novo design protein
  • Ligand: [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-2-phenyl-propanoate

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Supramolecule #1: M1 muscarinic acetylcholine receptor/de novo design fusion protein

SupramoleculeName: M1 muscarinic acetylcholine receptor/de novo design fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Muscarinic acetylcholine receptor M1,de novo design protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.835406 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDAMNT SAPPAVSPNI TVLAPGKGPW QVAFIGITTG LLSLATVTGN LLVLISFKVN TKLKTVNNYF LLSLACADLI IGTFSMNLY TTYLLMGHWA LGTLACDLWL ALDYVASNAS VMNLLLISFD RYFSVTRPLS YRAKRTPRRA ALMIGLAWLV S FVLWAPAI ...String:
DYKDDDAMNT SAPPAVSPNI TVLAPGKGPW QVAFIGITTG LLSLATVTGN LLVLISFKVN TKLKTVNNYF LLSLACADLI IGTFSMNLY TTYLLMGHWA LGTLACDLWL ALDYVASNAS VMNLLLISFD RYFSVTRPLS YRAKRTPRRA ALMIGLAWLV S FVLWAPAI LFWQYLVGER TVLAGQCYIQ FLSQPIITFG TAMAAFYLPV TVMCTLYWRI YRFRRRGAEA LERAFSLEDD KE ALLAALD ALAEAFADDA ELTALLALLR RLLEDPDLPA DELAALRAAL TRFPEFREAL LALLDRYLAT RDLADARDLV WAL VLAIAS DPRYRPAVAA MIAFGDAEVL RAGLLRGAEA LGLPGGEALV EEIMAEAEKE KKAARTLSAI LLAFILTWTP YNIM VLVST FCKDCVPETL WELGYWLCYV NSTININPMC YALCNINPMC YALCNINPMC YALCNHHHHH H

UniProtKB: Muscarinic acetylcholine receptor M1, Muscarinic acetylcholine receptor M1

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Macromolecule #2: [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-...

MacromoleculeName: [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-2-phenyl-propanoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EBT
Molecular weightTheoretical: 289.369 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: FLOOD BEAM / 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 AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121129
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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