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- EMDB-63998: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-63998
TitleCryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
Map data
Sample
  • Complex: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
    • Protein or peptide: M1 muscarinic acetylcholine receptor, 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 / atropine / de novo protein / MEMBRANE PROTEIN / nanobody
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 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 the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
Authors: Zhang X / Gao K / Liu X
History
DepositionApr 2, 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_63998.png

Downloads & links

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Map

FileDownload / File: emd_63998.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.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.7509346 - 4.873107
Average (Standard dev.)-0.0014058581 (±0.059342522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63998_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63998_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 : Cryo-EM structure of the M1 muscarinic acetylcholine receptor bou...

EntireName: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
Components
  • Complex: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
    • Protein or peptide: M1 muscarinic acetylcholine receptor, 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: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bou...

SupramoleculeName: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 54.691621 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAAA QTSAPPAVSP QITVLAPGKG PWQVAFIGIT TGLLSLATVT GNLLVLISFK VNTELKTVNN YFLLSLACAD LIIGTFSMN LYTTYLLMGH WALGTLACDL WLALDYVASN ASVMNLLLIS FDRYFSVTRP LSYRAKRTPR RAALMIGLAW L VSFVLWAP ...String:
DYKDDDDAAA QTSAPPAVSP QITVLAPGKG PWQVAFIGIT TGLLSLATVT GNLLVLISFK VNTELKTVNN YFLLSLACAD LIIGTFSMN LYTTYLLMGH WALGTLACDL WLALDYVASN ASVMNLLLIS FDRYFSVTRP LSYRAKRTPR RAALMIGLAW L VSFVLWAP AILFWQYLVG ERTVLAGQCY IQFLSQPIIT FGTAMAAFYL PVTVMCTLYW RIYRFRRRGA EALERAFSLE DD KEALLAA LDALAEAFAD DAELTALLAL LRRLLEDPDL PADELAALRA ALTRFPEFRE ALLALLDRYL ATRDLADARD LVW ALVLAI ASDPRYRPAV AAMIAFGDAE VLRAGLLRGA EALGLPGGEA LVEEIMAEAE KEKKAARTLS AILLAFILTW TPYN IMVLV STFCKDCVPE TLWELGYWLC YVNSTINPMC YALCNKAFRD TFRLLLLCRW DKRRWRKIPK RPGSVHRTPS RQCHH HHHH HHH

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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

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: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 254687
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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