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Yorodumi- EMDB-27344: cryo-EM structure of TRPM3 ion channel in complex with Gbg, tethe... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27344 | |||||||||
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Title | cryo-EM structure of TRPM3 ion channel in complex with Gbg, tethered by ALFA-nanobody | |||||||||
Map data | sharpened map with a B-factor of 112.4 | |||||||||
Sample |
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Function / homology | Function and homology information monoatomic cation transmembrane transport / monoatomic cation transport / monoatomic cation channel activity / calcium ion transmembrane transport / protein tetramerization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / calcium channel activity / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors ...monoatomic cation transmembrane transport / monoatomic cation transport / monoatomic cation channel activity / calcium ion transmembrane transport / protein tetramerization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / calcium channel activity / 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 / extracellular vesicle / G alpha (12/13) signalling events / 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 | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Zhao C / MacKinnon R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Neuron / Year: 2023 Title: Structural and functional analyses of a GPCR-inhibited ion channel TRPM3. Authors: Chen Zhao / Roderick MacKinnon / Abstract: G-protein coupled receptors (GPCRs) govern the physiological response to stimuli by modulating the activity of downstream effectors, including ion channels. TRPM3 is an ion channel inhibited by GPCRs ...G-protein coupled receptors (GPCRs) govern the physiological response to stimuli by modulating the activity of downstream effectors, including ion channels. TRPM3 is an ion channel inhibited by GPCRs through direct interaction with G protein (Gβγ) released upon their activation. This GPCR-TRPM3 signaling pathway contributes to the analgesic effect of morphine. Here, we characterized Gβγ inhibition of TRPM3 using electrophysiology and single particle cryo-electron microscopy (cryo-EM). From electrophysiology, we obtained a half inhibition constant (IC50) of ∼240 nM. Using cryo-EM, we determined structures of mouse TRPM3 expressed in human cells with and without Gβγ and with and without PIP, a lipid required for TRPM3 activity, at resolutions of 2.7-4.7 Å. Gβγ-TRPM3 interfaces vary depending on PIP occupancy; however, in all cases, Gβγ appears loosely attached to TRPM3. The IC50 in electrophysiology experiments raises the possibility that additional unknown factors may stabilize the TRPM3-Gβγ complex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27344.map.gz | 16.2 MB | EMDB map data format | |
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Header (meta data) | emd-27344-v30.xml emd-27344.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27344_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_27344.png | 101.6 KB | ||
Others | emd_27344_half_map_1.map.gz emd_27344_half_map_2.map.gz | 275.5 MB 275.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27344 | HTTPS FTP |
-Related structure data
Related structure data | 8ddwMC 8ddqC 8ddrC 8ddsC 8ddtC 8dduC 8ddvC 8ddxC 8ed7C 8ed8C 8ed9C 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_27344.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map with a B-factor of 112.4 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_27344_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_27344_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TRPM3
Entire | Name: TRPM3 |
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Components |
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-Supramolecule #1: TRPM3
Supramolecule | Name: TRPM3 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Transient receptor potential cation channel, subfamily M, member 3
Macromolecule | Name: Transient receptor potential cation channel, subfamily M, member 3 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 157.812922 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGKKWRDAGE LERGCSDRED SAESRRRSRS ASRGRFAESW KRLSSKQGST KRSGLPAQQT PAQKSWIERA FYKRECVHII PSTKDPHRC CCGRLIGQHV GLTPSISVLQ NEKNESRLSR NDIQSEKWSI SKHTQLSPTD AFGTIEFQGG GHSNKAMYVR V SFDTKPDL ...String: MGKKWRDAGE LERGCSDRED SAESRRRSRS ASRGRFAESW KRLSSKQGST KRSGLPAQQT PAQKSWIERA FYKRECVHII PSTKDPHRC CCGRLIGQHV GLTPSISVLQ NEKNESRLSR NDIQSEKWSI SKHTQLSPTD AFGTIEFQGG GHSNKAMYVR V SFDTKPDL LLHLMTKEWQ LELPKLLISV HGGLQNFELQ PKLKQVFGKG LIKAAMTTGA WIFTGGVNTG VIRHVGDALK DH ASKSRGK ICTIGIAPWG IVENQEDLIG RDVVRPYQTM SNPMSKLTVL NSMHSHFILA DNGTTGKYGA EVKLRRQLEK HIS LQKINT RIGQGVPVVA LIVEGGPNVI SIVLEYLRDT PPVPVVVCDG SGRASDILAF GHKYSEEGGL INESLRDQLL VTIQ KTFTY TRTQAQHLFI ILMECMKKKE LITVFRMGSE GHQDIDLAIL TALLKGANAS APDQLSLALA WNRVDIARSQ IFIYG QQWP VGSLEQAMLD ALVLDRVDFV KLLIENGVSM HRFLTISRLE ELYNTRHGPS NTLYHLVRDV KKGNLPPDYR ISLIDI GLV IEYLMGGAYR CNYTRKRFRT LYHNLFGPKR PKALKLLGME DDIPLRRGRK TTKKREEEVD IDLDDPEINH FPFPFHE LM VWAVLMKRQK MALFFWQHGE EAMAKALVAC KLCKAMAHEA SENDMVDDIS QELNHNSRDF GQLAVELLDQ SYKQDEQL A MKLLTYELKN WSNATCLQLA VAAKHRDFIA HTCSQMLLTD MWMGRLRMRK NSGLKVILGI LLPPSILSLE FKNKDDMPY MTQAQEIHLQ EKEPEEPEKP TKEKDEEDME LTAMLGRSNG ESSRKKDEEE VQSRHRLIPV GRKIYEFYNA PIVKFWFYTL AYIGYLMLF NYIVLVKMER WPSTQEWIVI SYIFTLGIEK MREILMSEPG KLLQKVKVWL QEYWNVTDLI AILLFSVGMI L RLQDQPFR SDGRVIYCVN IIYWYIRLLD IFGVNKYLGP YVMMIGKMMI DMMYFVIIML VVLMSFGVAR QAILFPNEEP SW KLAKNIF YMPYWMIYGE VFADQIDPPC GQNETREDGK TIQLPPCKTG AWIVPAIMAC YLLVANILLV NLLIAVFNNT FFE VKSISN QVWKFQRYQL IMTFHERPVL PPPLIIFSHM TMIFQHVCCR WRKHESDQDE RDYGLKLFIT DDELKKVHDF EEQC IEEYF REKDDRFNSS NDERIRVTSE RVENMSMRLE EVNEREHSMK ASLQTVDIRL AQLEDLIGRM ATALERLTGL ERAES NKIR SRTSSDCTDA AYIVRQSSFN SQEGNTFKLQ ESIDPAGEET ISPTSPTLMP RMRSHSFYSV NVKDKGGIEK LESIFK ERS LSLHRATS |
-Macromolecule #2: Unidentified segment at the N-terminus of TRPM3
Macromolecule | Name: Unidentified segment at the N-terminus of TRPM3 / type: protein_or_peptide / ID: 2 Details: a segment at the N-terminus of TRPM3 whose sequence cannot be identified from the cryo-EM density Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 1.464797 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) |
-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: 37.285734 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW ...String: SELDQLRQEA EQLKNQIRDA RKACADATLS QITNNIDPVG RIQMRTRRTL RGHLAKIYAM HWGTDSRLLV SASQDGKLII WDSYTTNKV HAIPLRSSWV MTCAYAPSGN YVACGGLDNI CSIYNLKTRE GNVRVSRELA GHTGYLSCCR FLDDNQIVTS S GDTTCALW DIETGQQTTT FTGHTGDVMS LSLAPDTRLF VSGACDASAK LWDVREGMCR QTFTGHESDI NAICFFPNGN AF ATGSDDA TCRLFDLRAD QELMTYSHDN IICGITSVSF SKSGRLLLAG YDDFNCNVWD ALKADRAGVL AGHDNRVSCL GVT DDGMAV ATGSWDSFLK IWN |
-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: 7.713882 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFSAIL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |