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- EMDB-35761: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex -

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Entry
Database: EMDB / ID: EMD-35761
TitleCryo-EM structure of the PEA-bound mTAAR9-Golf complex
Map data
Sample
  • Complex: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(olf) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Trace amine-associated receptor 9
    • Protein or peptide: scFv16
KeywordsPEA / mTAAR9 / MEMBRANE PROTEIN
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Amine ligand-binding receptors / trace-amine receptor activity / G alpha (s) signalling events / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization ...Adenylate cyclase activating pathway / Amine ligand-binding receptors / trace-amine receptor activity / G alpha (s) signalling events / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Regulation of insulin secretion / G protein-coupled receptor binding / Olfactory Signaling Pathway / G-protein beta/gamma-subunit complex binding / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / 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 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to peptide hormone / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / GDP binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / synapse / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Trace amine associated receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit ...Trace amine associated receptor family / G-protein alpha subunit, group S / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(olf) subunit alpha / 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(i) subunit alpha-1 / Trace amine-associated receptor 9
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSun JP / Li Q / Yang F / Xu YF / Guo LL / Lian S / Zhang MH / Rong NK
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFC1003600 China
CitationJournal: Nature / Year: 2023
Title: Structural basis of amine odorant perception by a mammal olfactory receptor.
Authors: Lulu Guo / Jie Cheng / Shuo Lian / Qun Liu / Yan Lu / Yuan Zheng / Kongkai Zhu / Minghui Zhang / Yalei Kong / Chao Zhang / Naikang Rong / Yuming Zhuang / Guoxing Fang / Jingjing Jiang / ...Authors: Lulu Guo / Jie Cheng / Shuo Lian / Qun Liu / Yan Lu / Yuan Zheng / Kongkai Zhu / Minghui Zhang / Yalei Kong / Chao Zhang / Naikang Rong / Yuming Zhuang / Guoxing Fang / Jingjing Jiang / Tianyao Zhang / Xiang Han / Zili Liu / Ming Xia / Shangming Liu / Lei Zhang / Stephen D Liberles / Xiao Yu / Yunfei Xu / Fan Yang / Qian Li / Jin-Peng Sun /
Abstract: Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors (TAARs). TAARs emerged ...Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors (TAARs). TAARs emerged following the divergence of jawed and jawless fish, and comprise a large monophyletic family of receptors that recognize volatile amine odorants to elicit both intraspecific and interspecific innate behaviours such as attraction and aversion. Here we report cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and mTAAR9-G or mTAAR9-G trimers in complex with β-phenylethylamine, N,N-dimethylcyclohexylamine or spermidine. The mTAAR9 structures contain a deep and tight ligand-binding pocket decorated with a conserved DWY motif, which is essential for amine odorant recognition. In the mTAAR9 structure, a unique disulfide bond connecting the N terminus to ECL2 is required for agonist-induced receptor activation. We identify key structural motifs of TAAR family members for detecting monoamines and polyamines and the shared sequence of different TAAR members that are responsible for recognition of the same odour chemical. We elucidate the molecular basis of mTAAR9 coupling to G and G by structural characterization and mutational analysis. Collectively, our results provide a structural basis for odorant detection, receptor activation and G coupling of an amine olfactory receptor.
History
DepositionMar 29, 2023-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35761.png

Downloads & links

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Map

FileDownload / File: emd_35761.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017833437 - 2.094909
Average (Standard dev.)0.003962372 (±0.043043744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 170.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35761_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_35761_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the PEA-bound mTAAR9-Golf complex

EntireName: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex
Components
  • Complex: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(olf) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Trace amine-associated receptor 9
    • Protein or peptide: scFv16

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Supramolecule #1: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex

SupramoleculeName: Cryo-EM structure of the PEA-bound mTAAR9-Golf complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine n...

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(olf) subunit alpha
type: protein_or_peptide / ID: 1
Details: Author stated: We buide a chimera based on wide type Guanine nucleotide-binding protein G(olf) subunit alpha and deleted GaAH domain (V67-L190) according to the Articles (Nehme, Rony et al. ...Details: Author stated: We buide a chimera based on wide type Guanine nucleotide-binding protein G(olf) subunit alpha and deleted GaAH domain (V67-L190) according to the Articles (Nehme, Rony et al. "Mini-G proteins: Novel tools for studying GPCRs in their active conformation." PloS one vol. 12,4 e0175642. 20 Apr. 2017). Those residues (A236, S239, L259, I359, V362) are dominant negative mutant during G protein modification to increase stability and affinity. A modified Gaolf chimera (Chain A) was generated on the basis of the mini-Golf scaffold with its N terminus replaced by the N terminus of Golf (residue M1 to residue K27) with Gai1 (residue M1 to residue M18) to facilitate the binding of scFv16.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.528566 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKERLAY KATHRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETRFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIYV ADCSDYNMVI REDNNTNRLR ESLDDFESIW NNRWLRTISI ILFLNKQDML A EKVLAGKS ...String:
MGCTLSAEDK AAVERSKMIE KQLQKERLAY KATHRLLLLG ADNSGKSTIV KQMRILHGGS GGSGGTSGIF ETRFQVDKVN FHMFDVGGQ RDERRKWIQC FNDVTAIIYV ADCSDYNMVI REDNNTNRLR ESLDDFESIW NNRWLRTISI ILFLNKQDML A EKVLAGKS KIEDYFPEYA NYTVPEDATP DAGEDPKVTR AKFFIRDLFL RISTATGDGK HYCYPHFTCA VDTENARRIF ND CRDIIQR MHLKQYELL

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

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2
Details: Author stated: residues (-9) - (-4) is His Tag, residues 341-355 is Linker, residues 356-366 is Small Bit.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.055867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWNGSSGG GGSGGGGSSG VSGWRLFKKI S

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.504446 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFRE

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Macromolecule #4: Trace amine-associated receptor 9

MacromoleculeName: Trace amine-associated receptor 9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 38.928238 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTSDFSPEPP MELCYENVNG SCIKSSYAPW PRAILYGVLG LGALLAVFGN LLVIIAILHF KQLHTPTNFL VASLACADFL VGVTVMPFS TVRSVESCWY FGESYCKFHT CFDTSFCFAS LFHLCCISID RYIAVTDPLT YPTKFTVSVS GLCIALSWFF S VTYSFSIF ...String:
MTSDFSPEPP MELCYENVNG SCIKSSYAPW PRAILYGVLG LGALLAVFGN LLVIIAILHF KQLHTPTNFL VASLACADFL VGVTVMPFS TVRSVESCWY FGESYCKFHT CFDTSFCFAS LFHLCCISID RYIAVTDPLT YPTKFTVSVS GLCIALSWFF S VTYSFSIF YTGANEEGIE ELVVALTCVG GCQAPLNQNW VLLCFLLFFL PTVVMVFLYG RIFLVAKYQA RKIEGTANQA QA SSESYKE RVAKRERKAA KTLGIAMAAF LVSWLPYIID AVIDAYMNFI TPAYVYEILV WCVYYNSAMN PLIYAFFYPW FRK AIKLIV SGKVFRADSS TTNLFSEEAG AG

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Macromolecule #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 30.363043 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSAG G GGSGGGGS GGGGSADIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DR FSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GAGTKLEL

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.875 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 749097

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