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- PDB-9m55: Structural insight into determinants of endogenous agonist select... -

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Basic information

Entry
Database: PDB / ID: 9m55
TitleStructural insight into determinants of endogenous agonist selectivity of aminergic receptors from octopamine b2 receptor structure
Components
  • G-protein gamma subunit
  • G-protein subunit alpha
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • octopamine b2 receptor
  • single chain Fv 16
KeywordsSIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 ...Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of taste / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat ...G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesIxodes scapularis (black-legged tick)
Homo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHori, T. / Katsuta, K. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05046 Japan
CitationJournal: PNAS Nexus / Year: 2025
Title: Structural insights into endogenous agonist selectivity of aminergic receptors from the octopamine β receptor.
Authors: Tetsuya Hori / Kazushige Katsura / Sayako Miyamoto-Kohno / Tomomi Uchikubo-Kamo / Mayumi Yonemochi / Mikako Shirouzu /
Abstract: Tyrosine-derived amines (TDAs), such as octopamine, noradrenaline, dopamine, and tyramine, are essential neurotransmitters that play diverse roles in various physiological processes. The distinct ...Tyrosine-derived amines (TDAs), such as octopamine, noradrenaline, dopamine, and tyramine, are essential neurotransmitters that play diverse roles in various physiological processes. The distinct receptor selectivity of these structurally similar molecules is vital for their specific functions. However, all these receptors belong to the same subfamily of G-protein-coupled receptors and share high sequence homology within their orthosteric binding sites. The molecular basis of this selectivity remains unclear because of the absence of structural data on octopamine and tyramine receptors. In this study, we present cryo-electron microscopy structures of the deer tick octopamine β receptor (octβR) bound to octopamine or -2,4-dimethylphenyl-'-methylformamidine (DPMF), an acaricidal amitraz metabolite. Octopamine and DPMF formed aromatic interactions with Y307 and F328, residues crucial for octβR activation. The lower potency of other TDAs for octβR stems from the subtle effect of functional groups on both interactions, i.e. the meta-hydroxyl group of noradrenaline and dopamine hinders edge-to-edge interaction with Y307, and the absence of a 1-hydroxyl group in dopamine and tyramine prevents π-hydrogen bonding with F328. These structural insights into octβR selectivity are likely applicable across other TDA receptors, highlighting the pivotal role of residues 6.55 and 7.39. Consequently, the elucidated selection mechanism provides fundamental knowledge of aminergic ligand recognition, a process crucial for neurotransmission and overall organismal function.
History
DepositionMar 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein subunit alpha
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: G-protein gamma subunit
R: octopamine b2 receptor
S: single chain Fv 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,0436
Polymers178,8815
Non-polymers1621
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

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Protein , 4 types, 4 molecules ABGR

#1: Protein G-protein subunit alpha


Mass: 47011.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Production host: Escherichia coli (E. coli)
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 39541.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda granulovirus / References: UniProt: P62873
#3: Protein G-protein gamma subunit


Mass: 11222.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda granulovirus
#4: Protein octopamine b2 receptor


Mass: 48186.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Production host: Spodoptera frugiperda granulovirus

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Antibody / Non-polymers , 2 types, 2 molecules S

#5: Antibody single chain Fv 16


Mass: 32919.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): cell-free / Production host: Escherichia coli (E. coli)
#6: Chemical ChemComp-A1L8N / ~{N}'-(2,4-dimethylphenyl)-~{N}-methyl-methanimidamide


Mass: 162.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: GPCR and G-protein complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Ixodes scapularis (black-legged tick)
Source (recombinant)Organism: Spodoptera frugiperda granulovirus
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246183 / Symmetry type: POINT

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