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- EMDB-64050: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64050
Titlecryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4
Map data
Sample
  • Complex: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4/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
    • Protein or peptide: Nanobody Nb1B4
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
KeywordsGPCR / active-state / nanobody / de novo protein / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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 M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4
Authors: Zhang X / Gao K / Liu X
History
DepositionApr 5, 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_64050.png

Downloads & links

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Map

FileDownload / File: emd_64050.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)

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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-4.1961503 - 5.653426
Average (Standard dev.)0.00056715833 (±0.07878575)
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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Mask #1

Fileemd_64050_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_64050_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_64050_half_map_2.map
Projections & Slices
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Sample components

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Entire : cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 ...

EntireName: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4/de novo design fusion protein
Components
  • Complex: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4/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
    • Protein or peptide: Nanobody Nb1B4
  • Ligand: 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium

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Supramolecule #1: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 ...

SupramoleculeName: cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4/de novo design fusion protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 49.317816 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 RIYRETKRAG ERLAKLLEKF EA LPLEDIV AALKALLATN RPEIQLAVKT IVENFPEIKK EAEKLTPEQK AKLAALEAQL ADLPEELRKV LLSMYLTGLL YGG SEENRK RAIEKAARTL SAILLAFILT WTPYNIMVLV STFCKDCVPE TLWELGYWLC YVNSTINPMC YALCNKAFRD TFRL LLLCR WDKRRWRKIP KRPGSVHRTP SRQCHHHHHH

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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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Macromolecule #3: Nanobody Nb1B4

MacromoleculeName: Nanobody Nb1B4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.766307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGSIFY GYYMGWYRQA PGKEREFVAT INYGASTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAVRR VYVYVQRYYH YYWGQGTQVT VSS

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Macromolecule #4: 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: 4 / 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: 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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 191008
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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