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Yorodumi- EMDB-17756: Structure of the murine trace amine-associated receptor TAAR7f bo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17756 | |||||||||
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Title | Structure of the murine trace amine-associated receptor TAAR7f bound to N,N-dimethylcyclohexylamine (DMCH) in complex with mini-Gs trimeric G protein | |||||||||
Map data | Consensus map of the mTAAR7f receptor bound to NDMCH in complex with miniGs trimer | |||||||||
Sample |
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Keywords | trace-amine associated receptor / TAAR / mTAAR7f / GPCR / receptor / G protein / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information trace-amine receptor activity / sensory perception of chemical stimulus / 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 activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels ...trace-amine receptor activity / sensory perception of chemical stimulus / 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 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 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
Authors | Gusach A / Lee Y / Edwards PC / Huang F / Weyand SN / Tate CG | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: bioRxiv / Year: 2023 Title: Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f. Authors: Anastasiia Gusach / Yang Lee / Armin Nikpour Khoshgrudi / Elizaveta Mukhaleva / Ning Ma / Eline J Koers / Qingchao Chen / Patricia C Edwards / Fanglu Huang / Jonathan Kim / Filippo Mancia / ...Authors: Anastasiia Gusach / Yang Lee / Armin Nikpour Khoshgrudi / Elizaveta Mukhaleva / Ning Ma / Eline J Koers / Qingchao Chen / Patricia C Edwards / Fanglu Huang / Jonathan Kim / Filippo Mancia / Dmitry B Verprintsev / Nagarajan Vaidehi / Simone N Weyand / Christopher G Tate / Abstract: There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are ...There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein G and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 Å. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17756.map.gz | 93 MB | EMDB map data format | |
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Header (meta data) | emd-17756-v30.xml emd-17756.xml | 29.1 KB 29.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17756_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_17756.png | 121 KB | ||
Masks | emd_17756_msk_1.map emd_17756_msk_2.map | 196.4 MB 196.4 MB | Mask map | |
Filedesc metadata | emd-17756.cif.gz | 8 KB | ||
Others | emd_17756_additional_1.map.gz emd_17756_half_map_1.map.gz emd_17756_half_map_2.map.gz | 93.6 MB 182.4 MB 182.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17756 | HTTPS FTP |
-Validation report
Summary document | emd_17756_validation.pdf.gz | 937.3 KB | Display | EMDB validaton report |
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Full document | emd_17756_full_validation.pdf.gz | 936.9 KB | Display | |
Data in XML | emd_17756_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_17756_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17756 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17756 | HTTPS FTP |
-Related structure data
Related structure data | 8pm2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17756.map.gz / Format: CCP4 / Size: 196.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Consensus map of the mTAAR7f receptor bound to NDMCH in complex with miniGs trimer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17756_msk_1.map | ||||||||||||
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Density Histograms |
-Mask #2
File | emd_17756_msk_2.map | ||||||||||||
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Density Histograms |
-Additional map: Receptor-focused map
File | emd_17756_additional_1.map | ||||||||||||
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Annotation | Receptor-focused map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of the consensus map
File | emd_17756_half_map_1.map | ||||||||||||
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Annotation | Half map B of the consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of the consensus map
File | emd_17756_half_map_2.map | ||||||||||||
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Annotation | Half map A of the consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A complex of mouse trace-amine associated receptor 7f solubilized...
Entire | Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit ...Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 + Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 + Nanobody 35 |
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Components |
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-Supramolecule #1: A complex of mouse trace-amine associated receptor 7f solubilized...
Supramolecule | Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit ...Name: A complex of mouse trace-amine associated receptor 7f solubilized in LMNG/CHS bound to N,N-dimethylcyclohexylamine and coupled to: Engineered guanine nucleotide-binding protein G(s) subunit alpha isoform short + Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 + Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 + Nanobody 35 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.964734 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKLEDYFP ...String: GNSKTEDQRN EEKAQREANK KIEKQLQKDK QVYRATHRLL LLGADNSGKS TIVKQMRILH GGSGGSGGTS GIFETKFQVD KVNFHMFDV GGQRDERRKW IQCFNDVTAI IFVVDSSDYN RLQEALNLFK SIWNNRWLRT ISVILFLNKQ DLLAEKVLAG K SKLEDYFP EFARYTTPED ATPEPGEDPR VTRAKYFIRD EFLRISTASG DGRHYCYPHF TCAVDTENAR RIFNDCRDII QR MHLRQYE LL |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.342785 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 3 / Details: There is an engineered mutation C68S introduced / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.845078 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #4: Nanobody 35
Macromolecule | Name: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 16.926076 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MKYLLPTAAA GLLLLAAQPA MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGR FTISRDNAKN TLYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHH |
-Macromolecule #5: Trace amine-associated receptor 7f
Macromolecule | Name: Trace amine-associated receptor 7f / type: protein_or_peptide / ID: 5 Details: mTAAR7f sequence contains cleaved protease sites: TEV (S residue on the N terminus) and HRV-3C (C terminus) Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 41.012539 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: SMSIADETVS WNQDSILSRD LFSATSAELC YENLNRSCVR SPYSPGPRLI LYAVFGFGAV LAVCGNLLVM TSILHFRQLH SPANFLVAS LACADFLVGV MVMPFSMVRS VEGCWYFGDS YCKLHTCFDV SFCYCSLFHL CFISVDRYIA VSDPLAYPTR F TASVSGKC ...String: SMSIADETVS WNQDSILSRD LFSATSAELC YENLNRSCVR SPYSPGPRLI LYAVFGFGAV LAVCGNLLVM TSILHFRQLH SPANFLVAS LACADFLVGV MVMPFSMVRS VEGCWYFGDS YCKLHTCFDV SFCYCSLFHL CFISVDRYIA VSDPLAYPTR F TASVSGKC ITFSWLLSIS YGFSLIYTGA SEAGLEDLVS SLTCVGGCQI AVNQTWVFIN FSVFLIPTLV MITVYSKIFL IA KQQAQNI EKMSKQTARA SDSYKDRVAK RERKAAKTLG IAVAAFLLSW LPYFIDSFID AFLGFITPTY VYEILVWIVY YNS AMNPLI YAFFYPWFRK AIKLTVTGKI LRENSSTTNL FSELEVLFQ UniProtKB: Trace amine-associated receptor 7f |
-Macromolecule #6: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Macromolecule #7: ~{N},~{N}-dimethylcyclohexanamine
Macromolecule | Name: ~{N},~{N}-dimethylcyclohexanamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: 8IA |
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Molecular weight | Theoretical: 127.227 Da |
Chemical component information | ChemComp-8IA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER Details: Forward Power of 38 W, Reflected Power of 2W; Fischione | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11157 / Average exposure time: 7.84 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 2.4 µm / Calibrated magnification: 96000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: other Details: Initial models of heterotrimeric mini-Gs and Nb35 were sourced from PDB 7T9I. A de novo model of TAAR7f was generated from the focused map and protein sequence using ModelAngelo |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-8pm2: |