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- PDB-8uhb: Cryo-EM Structure of the Ro5256390-bound hTA1-Gs heterotrimer sig... -

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Basic information

Entry
Database: PDB / ID: 8uhb
TitleCryo-EM Structure of the Ro5256390-bound hTA1-Gs heterotrimer signaling complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Nanobody 35
  • Soluble cytochrome b562,Beta-2 adrenergic receptor,Trace amine-associated receptor 1
KeywordsMEMBRANE PROTEIN / GPCR / Signaling Complex / Trace Amine-associated Receptor
Function / homology
Function and homology information


adenylate cyclase regulator activity / regulation of parathyroid hormone secretion / COPI-coated Golgi to ER transport vesicle / post-embryonic body morphogenesis / Amine ligand-binding receptors / response to parathyroid hormone / trace-amine receptor activity / genomic imprinting / sensory perception of chemical stimulus / mu-type opioid receptor binding ...adenylate cyclase regulator activity / regulation of parathyroid hormone secretion / COPI-coated Golgi to ER transport vesicle / post-embryonic body morphogenesis / Amine ligand-binding receptors / response to parathyroid hormone / trace-amine receptor activity / genomic imprinting / sensory perception of chemical stimulus / mu-type opioid receptor binding / tissue homeostasis / positive regulation of sodium ion transport / endochondral ossification / corticotropin-releasing hormone receptor 1 binding / energy reserve metabolic process / embryonic cranial skeleton morphogenesis / positive regulation of osteoclast differentiation / beta2-adrenergic receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of mini excitatory postsynaptic potential / embryonic hindlimb morphogenesis / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / cartilage development / norepinephrine binding / positive regulation of autophagosome maturation / heat generation / Adrenoceptors / alkylglycerophosphoethanolamine phosphodiesterase activity / activation of transmembrane receptor protein tyrosine kinase activity / beta-2 adrenergic receptor binding / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / skin development / response to psychosocial stress / endosome to lysosome transport / adrenergic receptor signaling pathway / diet induced thermogenesis / positive regulation of protein kinase A signaling / neuronal dense core vesicle / hair follicle placode formation / adenylate cyclase binding / developmental growth / smooth muscle contraction / D1 dopamine receptor binding / regulation of signal transduction / G-protein alpha-subunit binding / alpha-tubulin binding / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / cellular response to glucagon stimulus / ruffle / insulin-like growth factor receptor binding / negative regulation of blood pressure / adenylate cyclase activator activity / ionotropic glutamate receptor binding / response to cold / receptor-mediated endocytosis / post-embryonic development / trans-Golgi network membrane / skeletal system development / G protein-coupled receptor activity / electron transport chain / clathrin-coated endocytic vesicle membrane / bone development / positive regulation of protein serine/threonine kinase activity / positive regulation of insulin secretion / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / multicellular organism growth / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / recycling endosome / sarcolemma / G protein activity / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / platelet aggregation / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / cognition / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane
Similarity search - Function
Trace amine associated receptor 1 / Trace amine associated receptor family / : / Beta 2 adrenoceptor / Adrenoceptor family / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group S / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx ...Trace amine associated receptor 1 / Trace amine associated receptor family / : / Beta 2 adrenoceptor / Adrenoceptor family / Cytochrome b562 / Cytochrome b562 / G-protein alpha subunit, group S / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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) / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-WV8 / Beta-2 adrenergic receptor / Soluble cytochrome b562 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Trace amine-associated receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsZilberg, G. / Warren, A.L. / Parpounas, A.K. / Wacker, D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133504 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH132317 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA053558 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM062754 United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular basis of human trace amine-associated receptor 1 activation.
Authors: Gregory Zilberg / Alexandra K Parpounas / Audrey L Warren / Shifan Yang / Daniel Wacker /
Abstract: The human trace amine-associated receptor 1 (hTAAR1, hTA1) is a key regulator of monoaminergic neurotransmission and the actions of psychostimulants. Despite preclinical research demonstrating its ...The human trace amine-associated receptor 1 (hTAAR1, hTA1) is a key regulator of monoaminergic neurotransmission and the actions of psychostimulants. Despite preclinical research demonstrating its tractability as a drug target, its molecular mechanisms of activation remain unclear. Moreover, poorly understood pharmacological differences between rodent and human TA1 complicate the translation of findings from preclinical disease models into novel pharmacotherapies. To elucidate hTA1's mechanisms on the molecular scale and investigate the underpinnings of its divergent pharmacology from rodent orthologs, we herein report the structure of the human TA1 receptor in complex with a Gαs heterotrimer. Our structure reveals shared structural elements with other TAARs, as well as with its closest monoaminergic orthologue, the serotonin receptor 5-HT4R. We further find that a single mutation dramatically shifts the selectivity of hTA1 towards that of its rodent orthologues, and report on the effects of substituting residues to those found in serotonin and dopamine receptors. Strikingly, we also discover that the atypical antipsychotic medication and pan-monoaminergic antagonist asenapine potently and efficaciously activates hTA1. Together our studies provide detailed insight into hTA1 structure and function, contrast its molecular pharmacology with that of related receptors, and uncover off-target activities of monoaminergic drugs at hTA1.
History
DepositionOct 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562,Beta-2 adrenergic receptor,Trace amine-associated receptor 1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanobody 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,0356
Polymers167,8175
Non-polymers2181
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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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCG

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 39418.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short


Mass: 45803.598 Da / Num. of mol.: 1
Mutation: E189D, M191V, T193S, E194D, N271K, K274D, R280K, T284D, I285T, G226A, A366S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnas / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63095
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Protein / Antibody / Non-polymers , 3 types, 3 molecules AN

#1: Protein Soluble cytochrome b562,Beta-2 adrenergic receptor,Trace amine-associated receptor 1 / Cytochrome b-562


Mass: 60019.816 Da / Num. of mol.: 1 / Mutation: M(-129)W, R(-14)G, Q(-3)E, F112W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: cybC, ADRB2, TAAR1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0ABE7, UniProt: P07550, UniProt: Q96RJ0
#5: Antibody Nanobody 35


Mass: 14714.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Chemical ChemComp-WV8 / (2R,4S)-4-[(2S)-2-phenylbutyl]-1,3-oxazolidin-2-amine


Mass: 218.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N2O / 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: hTA1-Gs-Nb35 complex (Ro5256390) / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9
Buffer solutionpH: 7.4
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen 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: 500 nm
Image recordingElectron dose: 53.88 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626370 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00516759
ELECTRON MICROSCOPYf_angle_d0.61830113
ELECTRON MICROSCOPYf_dihedral_angle_d17.0826811
ELECTRON MICROSCOPYf_chiral_restr0.0431304
ELECTRON MICROSCOPYf_plane_restr0.0032517

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