+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32824 | |||||||||||||||||||||
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Title | Cryo-EM structure of the human EP3-Gi signaling complex | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | GPCR / signal transduction / MEMBRANE PROTEIN / SIGNALING PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex ...negative regulation of gastric acid secretion / intestine smooth muscle contraction / prostaglandin E receptor activity / Prostanoid ligand receptors / cell death / positive regulation of fever generation / T cell migration / D2 dopamine receptor binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / Regulation of insulin secretion / G protein-coupled receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / 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 / G beta:gamma signalling through CDC42 / response to peptide hormone / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GDP binding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / nuclear envelope / retina development in camera-type eye / Ca2+ pathway / cell cortex / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / midbody / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / inflammatory response / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / synapse / GTP binding / protein-containing complex binding / nucleolus / magnesium ion binding / signal transduction / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.375 Å | |||||||||||||||||||||
Authors | Suno R / Sugita Y | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Structural insights into the G protein selectivity revealed by the human EP3-G signaling complex. Authors: Ryoji Suno / Yukihiko Sugita / Kazushi Morimoto / Hiroko Takazaki / Hirokazu Tsujimoto / Mika Hirose / Chiyo Suno-Ikeda / Norimichi Nomura / Tomoya Hino / Asuka Inoue / Kenji Iwasaki / ...Authors: Ryoji Suno / Yukihiko Sugita / Kazushi Morimoto / Hiroko Takazaki / Hirokazu Tsujimoto / Mika Hirose / Chiyo Suno-Ikeda / Norimichi Nomura / Tomoya Hino / Asuka Inoue / Kenji Iwasaki / Takayuki Kato / So Iwata / Takuya Kobayashi / Abstract: Prostaglandin receptors have been implicated in a wide range of functions, including inflammation, immune response, reproduction, and cancer. Our group has previously determined the crystal structure ...Prostaglandin receptors have been implicated in a wide range of functions, including inflammation, immune response, reproduction, and cancer. Our group has previously determined the crystal structure of the active-like EP3 bound to its endogenous agonist, prostaglandin E. Here, we present the single-particle cryoelectron microscopy (cryo-EM) structure of the human EP3-G signaling complex at a resolution of 3.4 Å. The structure reveals the binding mode of G to EP3 and the structural changes induced in EP3 by G binding. In addition, we compare the structure of the EP3-G complex with other subtypes of prostaglandin receptors (EP2 and EP4) bound to G that have been previously reported and examine the differences in amino acid composition at the receptor-G protein interface. Mutational analysis reveals that the selectivity of the G protein depends on specific amino acid residues in the second intracellular loop and TM5. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32824.map.gz | 110.6 MB | EMDB map data format | |
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Header (meta data) | emd-32824-v30.xml emd-32824.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32824_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_32824.png | 41.4 KB | ||
Masks | emd_32824_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-32824.cif.gz | 6.6 KB | ||
Others | emd_32824_half_map_1.map.gz emd_32824_half_map_2.map.gz | 140.7 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32824 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32824 | HTTPS FTP |
-Validation report
Summary document | emd_32824_validation.pdf.gz | 830.9 KB | Display | EMDB validaton report |
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Full document | emd_32824_full_validation.pdf.gz | 830.4 KB | Display | |
Data in XML | emd_32824_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | emd_32824_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32824 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32824 | HTTPS FTP |
-Related structure data
Related structure data | 7wu9MC 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_32824.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_32824_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map 1
File | emd_32824_half_map_1.map | ||||||||||||
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Annotation | unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map 2
File | emd_32824_half_map_2.map | ||||||||||||
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Annotation | unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Prostaglandine E receptor EP3-Gi complex
Entire | Name: Prostaglandine E receptor EP3-Gi complex |
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Components |
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-Supramolecule #1: Prostaglandine E receptor EP3-Gi complex
Supramolecule | Name: Prostaglandine E receptor EP3-Gi complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Prostaglandine E receptor EP3-Gi complex
Supramolecule | Name: Prostaglandine E receptor EP3-Gi complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: scFv16
Supramolecule | Name: scFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Prostaglandin E2 receptor EP3 subtype
Macromolecule | Name: Prostaglandin E2 receptor EP3 subtype / 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: 36.175887 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GPTSCGSVSV AFPITMLLTG FVGNALAMLL VSRSYRRRES KRKKSFLLCI GWLALTDLVG QLLTTPVVIV VYLSKQRWEH IDPSGRLCT FFGLTMTVFG LSSLFIASAM AVERALAIRA PHWYASHMKT RITRAVLLGV WLASLAFALL PVLGVGQYTV Q WPGTWCFI ...String: GPTSCGSVSV AFPITMLLTG FVGNALAMLL VSRSYRRRES KRKKSFLLCI GWLALTDLVG QLLTTPVVIV VYLSKQRWEH IDPSGRLCT FFGLTMTVFG LSSLFIASAM AVERALAIRA PHWYASHMKT RITRAVLLGV WLASLAFALL PVLGVGQYTV Q WPGTWCFI STGRGGQGTS SSHNWGNLFF ASAFAFLGLL ALTVTFSCNL ATIKALVDRC RAKATASQSS AQWGRITTET AI QLMGIML VLSVCWSPLL IMMLKMIFQQ TSVEHCKTHT EKQKECNFFL IAVRLASLNQ ILDPWVYLLL RKILLRKFCQ LEL EVLFQ UniProtKB: Prostaglandin E2 receptor EP3 subtype |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-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: 40.427969 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GSGCTLSAED KAAVERSKMI DRNLREDGEK AAREVKLLLL GAGESGKSTI VKQMKIIHEA GYSEEECKQY KAVVYSNTIQ SIIAIIRAM GRLKIDFGDS ARADDARQLF VLAGAAEEGF MTAELAGVIK RLWKDSGVQA CFNRSREYQL NDSAAYYLND L DRIAQPNY ...String: GSGCTLSAED KAAVERSKMI DRNLREDGEK AAREVKLLLL GAGESGKSTI VKQMKIIHEA GYSEEECKQY KAVVYSNTIQ SIIAIIRAM GRLKIDFGDS ARADDARQLF VLAGAAEEGF MTAELAGVIK RLWKDSGVQA CFNRSREYQL NDSAAYYLND L DRIAQPNY IPTQQDVLRT RVKTTGIVET HFTFKDLHFK MFDVGGQRSE RKKWIHCFEG VTAIIFCVAL SDYDLVLAED EE MNRMHES MKLFDSICNN KWFTDTSIIL FLNKKDLFEE KIKKSPLTIC YPEYAGSNTY EEAAAYIQCQ FEDLNKRKDT KEI YTHFTC ATDTKNVQFV FDAVTDVIIK NNLKDCGLF UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1 |
-Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.728152 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #5: scFv16
Macromolecule | Name: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 27.318389 KDa |
Recombinant expression | Organism: Brevibacillus agri (bacteria) |
Sequence | String: 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 KGENLYFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.07 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |