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- EMDB-27343: cryo-EM structure of TRPM3 ion channel in the presence of PIP2, state4 -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | cryo-EM structure of TRPM3 ion channel in the presence of PIP2, state4 | |||||||||
![]() | sharpened map with a B-factor of 85.2 | |||||||||
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![]() | TRPM3 / ion channel / PIP2 / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() metal ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / monoatomic cation channel activity / protein tetramerization / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Zhao C / MacKinnon R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 203.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 169.2 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 199.6 MB 199.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ddvMC ![]() 8ddqC ![]() 8ddrC ![]() 8ddsC ![]() 8ddtC ![]() 8dduC ![]() 8ddwC ![]() 8ddxC ![]() 8ed7C ![]() 8ed8C ![]() 8ed9C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | sharpened map with a B-factor of 85.2 | ||||||||||||||||||||
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_27343_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_27343_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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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 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 157.681734 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GKKWRDAGEL ERGCSDREDS AESRRRSRSA SRGRFAESWK RLSSKQGSTK RSGLPAQQTP AQKSWIERAF YKRECVHIIP STKDPHRCC CGRLIGQHVG LTPSISVLQN EKNESRLSRN DIQSEKWSIS KHTQLSPTDA FGTIEFQGGG HSNKAMYVRV S FDTKPDLL ...String: GKKWRDAGEL ERGCSDREDS AESRRRSRSA SRGRFAESWK RLSSKQGSTK RSGLPAQQTP AQKSWIERAF YKRECVHIIP STKDPHRCC CGRLIGQHVG LTPSISVLQN EKNESRLSRN DIQSEKWSIS KHTQLSPTDA FGTIEFQGGG HSNKAMYVRV S FDTKPDLL LHLMTKEWQL ELPKLLISVH GGLQNFELQP KLKQVFGKGL IKAAMTTGAW IFTGGVNTGV IRHVGDALKD HA SKSRGKI CTIGIAPWGI VENQEDLIGR DVVRPYQTMS NPMSKLTVLN SMHSHFILAD NGTTGKYGAE VKLRRQLEKH ISL QKINTR IGQGVPVVAL IVEGGPNVIS IVLEYLRDTP PVPVVVCDGS GRASDILAFG HKYSEEGGLI NESLRDQLLV TIQK TFTYT RTQAQHLFII LMECMKKKEL ITVFRMGSEG HQDIDLAILT ALLKGANASA PDQLSLALAW NRVDIARSQI FIYGQ QWPV GSLEQAMLDA LVLDRVDFVK LLIENGVSMH RFLTISRLEE LYNTRHGPSN TLYHLVRDVK KGNLPPDYRI SLIDIG LVI EYLMGGAYRC NYTRKRFRTL YHNLFGPKRP KALKLLGMED DIPLRRGRKT TKKREEEVDI DLDDPEINHF PFPFHEL MV WAVLMKRQKM ALFFWQHGEE AMAKALVACK LCKAMAHEAS ENDMVDDISQ ELNHNSRDFG QLAVELLDQS YKQDEQLA M KLLTYELKNW SNATCLQLAV AAKHRDFIAH TCSQMLLTDM WMGRLRMRKN SGLKVILGIL LPPSILSLEF KNKDDMPYM TQAQEIHLQE KEPEEPEKPT KEKDEEDMEL TAMLGRSNGE SSRKKDEEEV QSRHRLIPVG RKIYEFYNAP IVKFWFYTLA YIGYLMLFN YIVLVKMERW PSTQEWIVIS YIFTLGIEKM REILMSEPGK LLQKVKVWLQ EYWNVTDLIA ILLFSVGMIL R LQDQPFRS DGRVIYCVNI IYWYIRLLDI FGVNKYLGPY VMMIGKMMID MMYFVIIMLV VLMSFGVARQ AILFPNEEPS WK LAKNIFY MPYWMIYGEV FADQIDPPCG QNETREDGKT IQLPPCKTGA WIVPAIMACY LLVANILLVN LLIAVFNNTF FEV KSISNQ VWKFQRYQLI MTFHERPVLP PPLIIFSHMT MIFQHVCCRW RKHESDQDER DYGLKLFITD DELKKVHDFE EQCI EEYFR EKDDRFNSSN DERIRVTSER VENMSMRLEE VNEREHSMKA SLQTVDIRLA QLEDLIGRMA TALERLTGLE RAESN KIRS RTSSDCTDAA YIVRQSSFNS QEGNTFKLQE SIDPAGEETI SPTSPTLMPR MRSHSFYSVN VKDKGGIEKL ESIFKE RSL SLHRATS UniProtKB: Transient receptor potential cation channel, subfamily M, member 3 |
-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: ![]() ![]() |
Molecular weight | Theoretical: 1.464797 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) |
-Macromolecule #3: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
Macromolecule | Name: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: 3PH |
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Molecular weight | Theoretical: 704.998 Da |
Chemical component information | ![]() ChemComp-3PH: |
-Macromolecule #4: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...
Macromolecule | Name: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en type: ligand / ID: 4 / Number of copies: 4 / Formula: 9Z9 |
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Molecular weight | Theoretical: 544.805 Da |
Chemical component information | ![]() ChemComp-9Z9: |
-Macromolecule #5: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
Macromolecule | Name: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate type: ligand / ID: 5 / Number of copies: 4 / Formula: PIO |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ![]() ChemComp-PIO: |
-Macromolecule #6: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 6 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |