+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27339 | |||||||||
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Title | cryo-EM structure of TRPM3 ion channel in the absence of PIP2 | |||||||||
Map data | sharpened map with a B-factor of 13.2 | |||||||||
Sample |
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Keywords | TRPM3 / ion channel / PIP2 / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information metal ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / monoatomic cation channel activity / protein tetramerization / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_27339.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-27339-v30.xml emd-27339.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27339_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_27339.png | 173.4 KB | ||
Filedesc metadata | emd-27339.cif.gz | 6.4 KB | ||
Others | emd_27339_half_map_1.map.gz emd_27339_half_map_2.map.gz | 254.4 MB 254.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27339 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27339 | HTTPS FTP |
-Validation report
Summary document | emd_27339_validation.pdf.gz | 827.4 KB | Display | EMDB validaton report |
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Full document | emd_27339_full_validation.pdf.gz | 826.9 KB | Display | |
Data in XML | emd_27339_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | emd_27339_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27339 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27339 | HTTPS FTP |
-Related structure data
Related structure data | 8ddrMC 8ddqC 8ddsC 8ddtC 8dduC 8ddvC 8ddwC 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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-Map
File | Download / File: emd_27339.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map with a B-factor of 13.2 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.046 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_27339_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_27339_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 / Parent: 0 / Macromolecule list: #1-#2 |
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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: 154.649328 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 MRSHSFYSV 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: 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: 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: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 5 / 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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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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Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 73.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |