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- EMDB-62486: Cryo-EM structure of GPCR16-Gi complex -

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Entry
Database: EMDB / ID: EMD-62486
TitleCryo-EM structure of GPCR16-Gi complex
Map data
Sample
  • Complex: Complex of GPCR with Gi1.
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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: Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2
    • Protein or peptide: scFv16
  • Ligand: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside
KeywordsGPCR / Complex / SIGNALING PROTEIN
Function / homology
Function and homology information


bitter taste receptor activity / detection of chemical stimulus involved in sensory perception of bitter taste / ganglioside catabolic process / Class C/3 (Metabotropic glutamate/pheromone receptors) / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration ...bitter taste receptor activity / detection of chemical stimulus involved in sensory perception of bitter taste / ganglioside catabolic process / Class C/3 (Metabotropic glutamate/pheromone receptors) / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / cellular response to forskolin / regulation of mitotic spindle organization / Regulation of insulin secretion / trans-Golgi network / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / G-protein beta/gamma-subunit complex binding / centriolar satellite / 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 / 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 / GDP binding / 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) / G protein activity / GTPase binding / Ca2+ pathway / retina development in camera-type eye / midbody / cell cortex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / fibroblast proliferation / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / ciliary basal body / G protein-coupled receptor signaling pathway / external side of plasma membrane / lysosomal membrane / cell division / GTPase activity / intracellular membrane-bounded organelle / synapse / centrosome / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular exosome / extracellular region
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
exo-alpha-sialidase / 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 / Taste receptor type 2 member 16
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWang X / Wu LJ / Hua T / Liu ZJ
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030104 China
CitationJournal: To Be Published
Title: Cryo-EM structure of GPCR16-Gi complex
Authors: Wang X / Wu LJ / Hua T / Liu ZJ
History
DepositionNov 22, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62486.png

Downloads & links

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Map

FileDownload / File: emd_62486.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0017881077 - 2.2001536
Average (Standard dev.)0.0013865277 (±0.02840838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62486_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_62486_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62486_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of GPCR with Gi1.

EntireName: Complex of GPCR with Gi1.
Components
  • Complex: Complex of GPCR with Gi1.
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • 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: Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2
    • Protein or peptide: scFv16
  • Ligand: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside

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Supramolecule #1: Complex of GPCR with Gi1.

SupramoleculeName: Complex of GPCR with Gi1. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.29393 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDKEN LYFQSMGCTL SAEDKAAVER SKMIDRNLRE DGEKAAREVK LLLLGAGESG KSTIVKQMKI IHEAGYSEEE CKQYKAVVY SNTIQSIIAI IRAMGRLKID FGDSARADDA RQLFVLAGAA EEGFMTAELA GVIKRLWKDS GVQACFNRSR E YQLNDSAA ...String:
DYKDDDDKEN LYFQSMGCTL SAEDKAAVER SKMIDRNLRE DGEKAAREVK LLLLGAGESG KSTIVKQMKI IHEAGYSEEE CKQYKAVVY SNTIQSIIAI IRAMGRLKID FGDSARADDA RQLFVLAGAA EEGFMTAELA GVIKRLWKDS GVQACFNRSR E YQLNDSAA YYLNDLDRIA QPNYIPTQQD VLRTRVKTTG IVETHFTFKD LHFKMFDVGG QRSERKKWIH CFEGVTAIIF CV ALSDYDL VLAEDEEMNR MHESMKLFDS ICNNKWFTDT SIILFLNKKD LFEEKIKKSP LTICYPEYAG SNTYEEAAAY IQC QFEDLN KRKDTKEIYT HFTCATDTKN VQFVFDAVTD VIIKNNLKDC GLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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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 / 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

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

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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: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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

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Macromolecule #4: Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member...

MacromoleculeName: Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113.855758 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAHHHHHH HHHHENLYFQ SAHHHHHHSS GLEVLFQGPP EGAALTEKTD IFESGRNGNP NKDGIKSYR IPALLKTDKG TLIAGADERR LHSSDWGDIG MVIRRSEDNG KTWGDRVTIT NLRDNPKASD PSIGSPVNID M VLVQDPET ...String:
MKTIIALSYI FCLVFADYKD DDDAHHHHHH HHHHENLYFQ SAHHHHHHSS GLEVLFQGPP EGAALTEKTD IFESGRNGNP NKDGIKSYR IPALLKTDKG TLIAGADERR LHSSDWGDIG MVIRRSEDNG KTWGDRVTIT NLRDNPKASD PSIGSPVNID M VLVQDPET KRIFSIYDMF PEGKGIFGMS SQKEEAYKKI DGKTYQILYR EGEKGAYTIR ENGTVYTPDG KATDYRVVVD PV KPAYSDK GDLYKGDQLL GNIYFTTNKT SPFRIAKDSY LWMSYSDDDG KTWSAPQDIT PMVKADWMKF LGVGPGTGIV LRN GPHKGR ILIPVYTTNN VSHLDGSQSS RVIYSDDHGK TWHAGEAVND NRQVDGQKIH SSTMNNRRAQ NTESTVVQLN NGDV KLFMR GLTGDLQVAT SKDGGVTWEK DIKRYPQVKD VYVQMSAIHT MHEGKEYIIL SNAGGPKREN GMVHLARVEE NGELT WLKH NPIQKGEFAY NSLQELGNGE YGILYEHTEK GQNAYTLSFR KFNWEFLSKN GSGSGIPIQL TVFFMIIYVL ESLTII VQS SLIVAVLGRE WLQVRRLMPV DMILISLGIS RFCLQWASML NNFCSYFNLN YVLCNLTITW EFFNILTFWL NSLLTVF YC IKVSSFTHHI FLWLRWRILR LFPWILLGCL MITCVTIIPS AIGNYIQIQL LTMEHLPRNS TVTDKLENFH QYQFQAHT V ALVIPFILFL ASTIFLMASL TKQIQHHSTG HCNPSMKARF TALRSLAVLF IVFTSYFLTI LITIIGTLFD KRCWLWVWE AFVYAFILMH STSLMLSSPT LKRILKGKCG SGSGGSGSGG SGSGGSGSGS SGGVFTLEDF VGDWEQTAAY NLDQVLEQGG VSSLLQNLA VSVTPIQRIV RSGENALKID IHVIIPYEGL SADQMAQIEE VFKVVYPVDD HHFKVILPYG TLVIDGVTPN M LNYFGRPY EGIAVFDGKK ITVTGTLWNG NKIIDERLIT PDGSMLFRVT INS

UniProtKB: exo-alpha-sialidase, Taste receptor type 2 member 16

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Macromolecule #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.66682 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAENLYFQ SHHHHHHHH

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Macromolecule #6: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside

MacromoleculeName: 2-(hydroxymethyl)phenyl beta-D-glucopyranoside / type: ligand / ID: 6 / Number of copies: 1 / Formula: SA0
Molecular weightTheoretical: 286.278 Da
Chemical component information

ChemComp-SA0:
2-(hydroxymethyl)phenyl beta-D-glucopyranoside

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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
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229493
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9kpf:
Cryo-EM structure of GPCR16-Gi complex

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