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- EMDB-33365: Cryo-EM structure of a class T GPCR in ligand-free state -

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Basic information

Entry
Database: EMDB / ID: EMD-33365
TitleCryo-EM structure of a class T GPCR in ligand-free state
Map data
Sample
  • Complex: Complex of GPCR and G protein
    • Protein or peptide: Endoglucanase H,Taste receptor type 2 member 46,Bitter taste receptor T2R46
    • Protein or peptide: Guanine nucleotide-binding protein G(t) subunit alpha-3
    • 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: Nanobody 35Single-domain antibody
Function / homology
Function and homology information


bitter taste receptor activity / detection of chemical stimulus involved in sensory perception of bitter taste / Class C/3 (Metabotropic glutamate/pheromone receptors) / ciliary membrane / cellulase / cellulase activity / cellulose catabolic process / G protein-coupled receptor activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade ...bitter taste receptor activity / detection of chemical stimulus involved in sensory perception of bitter taste / Class C/3 (Metabotropic glutamate/pheromone receptors) / ciliary membrane / cellulase / cellulase activity / cellulose catabolic process / G protein-coupled receptor activity / 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / 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 / 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 / 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
Taste receptor type 2 / Taste receptor protein (TAS2R) / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. ...Taste receptor type 2 / Taste receptor protein (TAS2R) / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / 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 beta WD-40 repeat / Glycoside hydrolase superfamily / 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
Similarity search - Domain/homology
cellulase / Taste receptor type 2 member 46 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLiu ZJ / Hua T / Xu WX / Wu LJ
Funding support China, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030104 China
National Science Foundation (NSF, China)32022038 China
National Science Foundation (NSF, China)31930060 China
National Science Foundation (NSF, China)31870744 China
CitationJournal: Science / Year: 2022
Title: Structural basis for strychnine activation of human bitter taste receptor TAS2R46.
Authors: Weixiu Xu / Lijie Wu / Shenhui Liu / Xiao Liu / Xiaoling Cao / Cui Zhou / Jinyi Zhang / You Fu / Yu Guo / Yiran Wu / Qiwen Tan / Ling Wang / Junlin Liu / Longquan Jiang / Zhongbo Fan / Yuan ...Authors: Weixiu Xu / Lijie Wu / Shenhui Liu / Xiao Liu / Xiaoling Cao / Cui Zhou / Jinyi Zhang / You Fu / Yu Guo / Yiran Wu / Qiwen Tan / Ling Wang / Junlin Liu / Longquan Jiang / Zhongbo Fan / Yuan Pei / Jingyi Yu / Jianjun Cheng / Suwen Zhao / Xiaojiang Hao / Zhi-Jie Liu / Tian Hua /
Abstract: Taste sensing is a sophisticated chemosensory process, and bitter taste perception is mediated by type 2 taste receptors (TAS2Rs), or class T G protein-coupled receptors. Understanding the detailed ...Taste sensing is a sophisticated chemosensory process, and bitter taste perception is mediated by type 2 taste receptors (TAS2Rs), or class T G protein-coupled receptors. Understanding the detailed molecular mechanisms behind taste sensation is hindered by a lack of experimental receptor structures. Here, we report the cryo-electron microscopy structures of human TAS2R46 complexed with chimeric mini-G protein gustducin, in both strychnine-bound and apo forms. Several features of TAS2R46 are disclosed, including distinct receptor structures that compare with known GPCRs, a new "toggle switch," activation-related motifs, and precoupling with mini-G protein gustducin. Furthermore, the dynamic extracellular and more-static intracellular parts of TAS2R46 suggest possible diverse ligand-recognition and activation processes. This study provides a basis for further exploration of other bitter taste receptors and their therapeutic applications.
History
DepositionMay 3, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33365.png

Downloads & links

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Map

FileDownload / File: emd_33365.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017055095 - 1.8693225
Average (Standard dev.)0.001079115 (±0.023011962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33365_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_33365_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of GPCR and G protein

EntireName: Complex of GPCR and G protein
Components
  • Complex: Complex of GPCR and G protein
    • Protein or peptide: Endoglucanase H,Taste receptor type 2 member 46,Bitter taste receptor T2R46
    • Protein or peptide: Guanine nucleotide-binding protein G(t) subunit alpha-3
    • 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: Nanobody 35Single-domain antibody

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Supramolecule #1: Complex of GPCR and G protein

SupramoleculeName: Complex of GPCR and G protein / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Endoglucanase H,Taste receptor type 2 member 46,Bitter taste rece...

MacromoleculeName: Endoglucanase H,Taste receptor type 2 member 46,Bitter taste receptor T2R46
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.116266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAHHHHHH HHHHENLYFQ SGRAMASNYN SGLKIGAWVG TQPSESAIKS FQELQGRKLD IVHQFINWS TDFSWVRPYA DAVYNNGSIL MITWEPWEYN TVDIKNGKAD AYITRMAQDM KAYGKEIWLR PLHAANGDWY P WAIGYSSR ...String:
MKTIIALSYI FCLVFADYKD DDDAHHHHHH HHHHENLYFQ SGRAMASNYN SGLKIGAWVG TQPSESAIKS FQELQGRKLD IVHQFINWS TDFSWVRPYA DAVYNNGSIL MITWEPWEYN TVDIKNGKAD AYITRMAQDM KAYGKEIWLR PLHAANGDWY P WAIGYSSR VNTNETYIAA FRHIVDIFRA NGATNVKWVF NVNCDNVGNG TSYLGHYPGD NYVDYTSIDG YNWGTTQSWG SQ WQSFDQV FSRAYQALAS INKPIIIAEF ASAEIGGNKA RWITEAYNSI RTSYNKVIAA VWFHENKETD WRINSSPEAL AAY REAIGA ITFLPIIFSI LIVVTFVIGN FANGFIALVN SIEWFKRQKI SFADQILTAL AVSRVGLLWV LVLNWYATEL NPAF NSIEV RITAYNVWAV INHFSNWLAT SLSIFYLLKI ANFSNLIFLH LKRRVKSVVL VILLGPLLFL VCHLFVINMN QIIWT KEYE GNMTWKIKLR SAMYLSNTTV TILANLVPFT LTLISFLLLI CSLCKHLKKM QLHGKGSQDP SMKVHIKALQ TVTSFL LLC AIYFLSIIMS VWSFESLENK PVFMFCEAIA FSYPSTHPFI LIWGNKKLKQ TFLSVLWHVR YWVKGEKPSS SGSGSSG SG SSVFTLEDFV GDWEQTAAYN LDQVLEQGGV SSLLQNLAVS VTPIQRIVRS GENALKIDIH VIIPYEGLSA DQMAQIEE V FKVVYPVDDH HFKVILPYGT LVIDGVTPNM LNYFGRPYEG IAVFDGKKIT VTGTLWNGNK IIDERLITPD GSMLFRVTI NS

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Macromolecule #2: Guanine nucleotide-binding protein G(t) subunit alpha-3

MacromoleculeName: Guanine nucleotide-binding protein G(t) subunit alpha-3
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.583334 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKE NLYFQSNSKT EDQRNEEKAQ REANKKIEKQ LQKDKQVYRA THRLLLLGAD NSGKSTIVKQ MRILHGGSGG SGGTSGIFE TKFQVDKVNF HMFDVGGQRD ERRKWIQCFN DVTAIIFVVD SSDYNRLQEA LNDFKSIWNN RWLRTISVIL F LNKQDLLA ...String:
MDYKDDDDKE NLYFQSNSKT EDQRNEEKAQ REANKKIEKQ LQKDKQVYRA THRLLLLGAD NSGKSTIVKQ MRILHGGSGG SGGTSGIFE TKFQVDKVNF HMFDVGGQRD ERRKWIQCFN DVTAIIFVVD SSDYNRLQEA LNDFKSIWNN RWLRTISVIL F LNKQDLLA EKVLAGKSKI EDYFPEFARY TTPEDATPEP GEDPRVTRAK YFIRDEFLRI STASGDGRHY CYPHFTCAVD TQ NVKFVFD AVTDIIIKEN LKDCGLF

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.728426 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE 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 KIWNGSSGGG GSGGGGSSGV SGWRLFKKIS

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #5: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.271938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQVQLQESGG GLVQPGGSLR LSCAASGFTF SNYKMNWVRQ APGKGLEWVS DISQSGASIS YTGSVKGRFT ISRDNAKNTL YLQMNSLKP EDTAVYYCAR CPAPFTRDCF DVTSTTYAYR GQGTQVTVSS HHHHHHEPEA

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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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: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176154

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7xp5:
Cryo-EM structure of a class T GPCR in ligand-free state

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