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- PDB-9uaz: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bou... -

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Basic information

Entry
Database: PDB / ID: 9uaz
TitleCryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
ComponentsM1 muscarinic acetylcholine receptor, de novo design protein
KeywordsMEMBRANE PROTEIN / GPCR / inactive-state / atropine / de novo protein / nanobody
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsZhang, X. / Gao, K. / Liu, X.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: M1 muscarinic acetylcholine receptor, de novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9812
Polymers54,6921
Non-polymers2891
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 54691.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Chemical ChemComp-A1EBT / [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-2-phenyl-propanoate / Atropine sulfate


Mass: 289.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO3
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the M1 muscarinic acetylcholine receptor bound to atropine and nanobody NbA12
Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254687 / Symmetry type: POINT

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