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- EMDB-60796: Cryo-EM structure of MT3-alpha1AAR -

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Basic information

Entry
Database: EMDB / ID: EMD-60796
TitleCryo-EM structure of MT3-alpha1AAR
Map data
Sample
  • Complex: MT3-alpha2AAR complex
    • Protein or peptide: Muscarinic toxin 3
    • Protein or peptide: Alpha-1A adrenergic receptor,Soluble cytochrome b562
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / pilomotor reflex / phospholipase C-activating adrenergic receptor signaling pathway / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of action potential ...negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / alpha1-adrenergic receptor activity / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / positive regulation of heart rate by epinephrine-norepinephrine / positive regulation of the force of heart contraction by epinephrine-norepinephrine / pilomotor reflex / phospholipase C-activating adrenergic receptor signaling pathway / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of action potential / positive regulation of smooth muscle contraction / adult heart development / Adrenoceptors / positive regulation of cardiac muscle hypertrophy / smooth muscle contraction / positive regulation of vasoconstriction / adenylate cyclase-activating adrenergic receptor signaling pathway / response to hormone / positive regulation of cardiac muscle contraction / negative regulation of autophagy / positive regulation of synaptic transmission, GABAergic / caveola / MAPK cascade / G alpha (12/13) signalling events / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / toxin activity / phospholipase C-activating G protein-coupled receptor signaling pathway / nuclear membrane / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / intracellular signal transduction / G protein-coupled receptor signaling pathway / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / apoptotic process / signal transduction / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alpha 1A adrenoceptor / Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Adrenoceptor family / Snake toxin-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx ...Alpha 1A adrenoceptor / Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Adrenoceptor family / Snake toxin-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
Alpha-1A adrenergic receptor / Muscarinic toxin 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Dendroaspis angusticeps (eastern green mamba)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhong YX / Tao HH / Tao YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of MT3-alpha2AAR
Authors: Zhong YX / Tao HH / Tao YY
History
DepositionJul 13, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60796.png

Downloads & links

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Map

FileDownload / File: emd_60796.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.516
Minimum - Maximum-2.6817858 - 4.0726213
Average (Standard dev.)-0.0005990788 (±0.062662065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60796_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_60796_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 : MT3-alpha2AAR complex

EntireName: MT3-alpha2AAR complex
Components
  • Complex: MT3-alpha2AAR complex
    • Protein or peptide: Muscarinic toxin 3
    • Protein or peptide: Alpha-1A adrenergic receptor,Soluble cytochrome b562

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Supramolecule #1: MT3-alpha2AAR complex

SupramoleculeName: MT3-alpha2AAR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Muscarinic toxin 3

MacromoleculeName: Muscarinic toxin 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dendroaspis angusticeps (eastern green mamba)
Molecular weightTheoretical: 7.396488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LTCVTKNTIF GITTENCPAG QNLCFKRWHY VIPRYTEITR GCAATCPIPE NYDSIHCCKT DKCNE

UniProtKB: Muscarinic toxin 3

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Macromolecule #2: Alpha-1A adrenergic receptor,Soluble cytochrome b562

MacromoleculeName: Alpha-1A adrenergic receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.96916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SGNASDSSNC TQPPAPVNIS KAILLGVILG GLILFGVLGN ILVILSVACH RHLHSVTHYY IVNLAVADLL LTSTVLPFSA IFEVLGYWA FGRVFCNIWA AVDVLCCTAS IMGLCIISID RYIGVSYPLR YPTIVTQRRG LMALLCVWAL SLVISIGPLF G WRQPAPED ...String:
SGNASDSSNC TQPPAPVNIS KAILLGVILG GLILFGVLGN ILVILSVACH RHLHSVTHYY IVNLAVADLL LTSTVLPFSA IFEVLGYWA FGRVFCNIWA AVDVLCCTAS IMGLCIISID RYIGVSYPLR YPTIVTQRRG LMALLCVWAL SLVISIGPLF G WRQPAPED ETICQINEEP GYVLFSALGS FYLPLAIILV MYCRVYVVAK RELADLEDNW ETLNDNLKVI EKADNAAQVK DA LTKMRAA ALDAQKASGS GSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLLKFSREK KAA KTLGIV VGCFVLCWLP FFLVMPIGSF FPDFKPSETV FKIVFWLGYL NSCINPIIYP CSSQEFKKAF QNVLKIAALK EKIA ALKEK IAALKEAEEK RASRLEEELR RRLTEGSHHH HHHHH

UniProtKB: Alpha-1A adrenergic receptor, Alpha-1A adrenergic receptor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 569644
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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