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- PDB-8hn1: Cryo-EM structure of AdTx1-alpha1AAR-Nb6 -

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Basic information

Entry
Database: PDB / ID: 8hn1
TitleCryo-EM structure of AdTx1-alpha1AAR-Nb6
Components
  • Alpha-1A adrenergic receptor
  • Nb6
  • Toxin AdTx1
KeywordsMEMBRANE PROTEIN / Toxin / alpha1AAR / GPCR
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 / positive regulation of vasoconstriction / smooth muscle contraction / 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 / cell-cell signaling / G alpha (12/13) signalling events / MAPK cascade / toxin activity / positive regulation of cytosolic calcium ion concentration / nuclear membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / 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 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. ...Alpha 1A adrenoceptor / 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 / Toxin AdTx1
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
Homo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiu, X. / Shi, M.
Funding support China, 2items
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, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Toxin AdTx1
A: Alpha-1A adrenergic receptor
D: Nb6


Theoretical massNumber of molelcules
Total (without water)61,3003
Polymers61,3003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Toxin AdTx1 / Rho-elapitoxin-Da1a / Rho-Da1a / Rho-EPTX-Da1a


Mass: 7743.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis angusticeps (eastern green mamba)
Production host: Trichoplusia (butterflies/moths) / References: UniProt: P85092
#2: Protein Alpha-1A adrenergic receptor / Alpha-1A adrenoreceptor / Alpha-1A adrenoceptor / Alpha-1C adrenergic receptor / Alpha-adrenergic receptor 1c


Mass: 38825.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRA1A, ADRA1C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35348
#3: Antibody Nb6


Mass: 14730.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: Complex of AdTx1-alpha1AAR-Nb6 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.1 MDa / Experimental 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 616710 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033646
ELECTRON MICROSCOPYf_angle_d0.5234960
ELECTRON MICROSCOPYf_dihedral_angle_d4.242502
ELECTRON MICROSCOPYf_chiral_restr0.04570
ELECTRON MICROSCOPYf_plane_restr0.004616

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