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- PDB-9k6l: Cryo-EM structure of GPCR16-Gi2 complex -

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Basic information

Entry
Database: PDB / ID: 9k6l
TitleCryo-EM structure of GPCR16-Gi2 complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • exo-alpha-sialidase,Taste receptor type 2 member 16,LgBiT
  • scFv16
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Tas2R16 / GPCR / Gi2 / Salicin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


bitter taste receptor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / negative regulation of calcium ion-dependent exocytosis / G protein-coupled adenosine receptor signaling pathway / negative regulation of adenylate cyclase activity / positive regulation of urine volume / ganglioside catabolic process / positive regulation of neural precursor cell proliferation / negative regulation of synaptic transmission ...bitter taste receptor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / negative regulation of calcium ion-dependent exocytosis / G protein-coupled adenosine receptor signaling pathway / negative regulation of adenylate cyclase activity / positive regulation of urine volume / ganglioside catabolic process / positive regulation of neural precursor cell proliferation / negative regulation of synaptic transmission / Class C/3 (Metabotropic glutamate/pheromone receptors) / oligosaccharide catabolic process / gamma-aminobutyric acid signaling pathway / exo-alpha-sialidase / neuronal dense core vesicle / exo-alpha-sialidase activity / negative regulation of apoptotic signaling pathway / regulation of calcium ion transport / Adenylate cyclase inhibitory pathway / positive regulation of vascular associated smooth muscle cell proliferation / response to nutrient / hippocampal mossy fiber to CA3 synapse / positive regulation of superoxide anion generation / Regulation of insulin secretion / trans-Golgi network / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / G beta:gamma signalling through CDC42 / 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / cell body / GTPase binding / Ca2+ pathway / retina development in camera-type eye / midbody / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / 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 / positive regulation of ERK1 and ERK2 cascade / ciliary basal body / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / lysosomal membrane / cell division / GTPase activity / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / synapse / centrosome / dendrite / protein-containing complex binding / GTP binding / endoplasmic reticulum / signal transduction / extracellular exosome
Similarity search - Function
: / Taste receptor type 2 / Taste receptor protein (TAS2R) / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family ...: / Taste receptor type 2 / Taste receptor protein (TAS2R) / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / Sialidase superfamily / LPXTG cell wall anchor domain / G-protein alpha subunit, group I / 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 / Concanavalin A-like lectin/glucanase domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-(hydroxymethyl)phenyl beta-D-glucopyranoside / exo-alpha-sialidase / Guanine nucleotide-binding protein G(i) subunit alpha-2 / 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 / Taste receptor type 2 member 16
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsWang, X. / Zhou, C. / Wu, L.J. / Hua, T. / Liu, Z.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of GPCR16-Gi2 complex
Authors: Wang, X. / Zhou, C. / Wu, L.J. / Hua, T. / Liu, Z.J.
History
DepositionOct 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i) subunit alpha-2
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
S: scFv16
R: exo-alpha-sialidase,Taste receptor type 2 member 16,LgBiT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,9596
Polymers230,6735
Non-polymers2861
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#1: Protein Guanine nucleotide-binding protein G(i) subunit alpha-2 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40560.895 Da / Num. of mol.: 1 / Mutation: S47N, G204A, A327S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI2, GNAI2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04899
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 39728.426 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 (fall armyworm) / References: UniProt: P62873
#3: 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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Antibody / Protein / Sugars , 3 types, 3 molecules SR

#4: Antibody scFv16


Mass: 28666.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Protein exo-alpha-sialidase,Taste receptor type 2 member 16,LgBiT / Neuraminidase A / T2R16


Mass: 113855.758 Da / Num. of mol.: 1 / Mutation: S133C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria), (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: nanA_2, SAMEA3353537_00427, TAS2R16 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A4J2AMT3, UniProt: Q9NYV7, exo-alpha-sialidase
#6: Sugar ChemComp-SA0 / 2-(hydroxymethyl)phenyl beta-D-glucopyranoside / Salicin / 2-(hydroxymethyl)phenyl beta-D-glucoside / 2-(hydroxymethyl)phenyl D-glucoside / 2-(hydroxymethyl)phenyl glucoside


Type: D-saccharide / Mass: 286.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O7 / 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: tas2r16 with gi2 / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
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: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1064319 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049108
ELECTRON MICROSCOPYf_angle_d0.75912339
ELECTRON MICROSCOPYf_dihedral_angle_d4.4151226
ELECTRON MICROSCOPYf_chiral_restr0.0451410
ELECTRON MICROSCOPYf_plane_restr0.0051542

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