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- EMDB-34906: Cryo-EM structure of AdTx1-alpha1AAR-Nb6 -

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Basic information

Entry
Database: EMDB / ID: EMD-34906
TitleCryo-EM structure of AdTx1-alpha1AAR-Nb6
Map data
Sample
  • Complex: Complex of AdTx1-alpha1AAR-Nb6
    • Protein or peptide: Toxin AdTx1
    • Protein or peptide: Alpha-1A adrenergic receptor
    • Protein or peptide: Nb6
KeywordsToxin / alpha1AAR / GPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / positive regulation of the force of heart contraction by epinephrine-norepinephrine / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / alpha1-adrenergic receptor activity / pilomotor reflex / positive regulation of heart rate by epinephrine-norepinephrine / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of protein kinase C signaling / positive regulation of action potential ...negative regulation of heart rate involved in baroreceptor response to increased systemic arterial blood pressure / positive regulation of the force of heart contraction by epinephrine-norepinephrine / norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure / alpha1-adrenergic receptor activity / pilomotor reflex / positive regulation of heart rate by epinephrine-norepinephrine / neuron-glial cell signaling / cell growth involved in cardiac muscle cell development / positive regulation of protein kinase C signaling / positive regulation of action potential / positive regulation of smooth muscle contraction / adult heart development / Adrenoceptors / calcium ion transport into cytosol / positive regulation of cardiac muscle hypertrophy / : / smooth muscle contraction / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of vasoconstriction / positive regulation of cardiac muscle contraction / negative regulation of autophagy / response to hormone / caveola / positive regulation of synaptic transmission, GABAergic / MAPK cascade / G alpha (12/13) signalling events / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / toxin activity / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / nuclear membrane / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / apoptotic process / signal transduction / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Alpha 1A adrenoceptor / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / 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 ...Alpha 1A adrenoceptor / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / 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 / Toxin AdTx1
Similarity search - Component
Biological speciesHomo sapiens (human) / Dendroaspis angusticeps (eastern green mamba) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiu X / Shi M
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122041 China
National Natural Science Foundation of China (NSFC)32100968 China
CitationJournal: To Be Published
Title: Cryo-EM structure of AdTx1-alpha1AAR-Nb6
Authors: Liu X / Shi M
History
DepositionDec 6, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34906.png

Downloads & links

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Map

FileDownload / File: emd_34906.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.893549 - 6.314351
Average (Standard dev.)-0.0012309162 (±0.11135664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34906_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_34906_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 : Complex of AdTx1-alpha1AAR-Nb6

EntireName: Complex of AdTx1-alpha1AAR-Nb6
Components
  • Complex: Complex of AdTx1-alpha1AAR-Nb6
    • Protein or peptide: Toxin AdTx1
    • Protein or peptide: Alpha-1A adrenergic receptor
    • Protein or peptide: Nb6

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Supramolecule #1: Complex of AdTx1-alpha1AAR-Nb6

SupramoleculeName: Complex of AdTx1-alpha1AAR-Nb6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Toxin AdTx1

MacromoleculeName: Toxin AdTx1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dendroaspis angusticeps (eastern green mamba)
Molecular weightTheoretical: 7.743749 KDa
Recombinant expressionOrganism: Trichoplusia (butterflies/moths)
SequenceString:
GPGSGSLTCV TSKSIFGITT EDCPDGQNLC FKRRHYVVPK IYDSTRGCAA TCPIPENYDS IHCCKTDKCN E

UniProtKB: Toxin AdTx1

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Macromolecule #2: Alpha-1A adrenergic receptor

MacromoleculeName: Alpha-1A adrenergic receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.825605 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAMV FLSGQASDSS QCTQPPAPVQ ISKAILLGVI LGGLILFGVL GNILVILSVA CHRHLHSVTH YYIVNLAVAD LLLTSTVLP FSAIFEVLGY WAFGRVFCNI WAAVDVLCCT ARIWGLCIIS IDRYIGVSYP LRYPTIVTQR RGLMALLCVW A LSLVISIG ...String:
DYKDDDDAMV FLSGQASDSS QCTQPPAPVQ ISKAILLGVI LGGLILFGVL GNILVILSVA CHRHLHSVTH YYIVNLAVAD LLLTSTVLP FSAIFEVLGY WAFGRVFCNI WAAVDVLCCT ARIWGLCIIS IDRYIGVSYP LRYPTIVTQR RGLMALLCVW A LSLVISIG PLFGWRQPAP EDETICQINE EPGYVLFSAL GSFYLPLAII LVMYCRVYVV AKRVRLLSGS REKDRNLRKA AK TLGIVVG CFVLCWLPFF LVMPIGSFFP DFKPSETVFK IVFWLGYLNS CINPIIYPCS SQEFKKAFQN VLRIQCLCRK QSS KHALGY TLHPPSQAVE GQHHHHHHHH

UniProtKB: Alpha-1A adrenergic receptor

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Macromolecule #3: Nb6

MacromoleculeName: Nb6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.730255 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQVQLQESG GGLVQAGESL RLSCAASGTI FRLYDMGWYR RVSGNQRELV ASITSGGSTK YGDSVKGRFT ISRDNAKNTV YLQMSSLKP EDTAVYYCNA EYRTGIWEEL LDGWGQGTQV TVSSHHHHHH EPEA

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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

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: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 616710
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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