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- EMDB-27342: cryo-EM structure of TRPM3 ion channel in the presence of PIP2, state3 -
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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, state3 | |||||||||
![]() | sharpened map with a B-factor of 81.6 | |||||||||
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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: 3.0 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 | ![]() | 203.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.8 KB 16.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 169.1 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 199.6 MB 199.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dduMC ![]() 8ddqC ![]() 8ddrC ![]() 8ddsC ![]() 8ddtC ![]() 8ddvC ![]() 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
File | ![]() | ||||||||||||||||||||
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Annotation | sharpened map with a B-factor of 81.6 | ||||||||||||||||||||
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_27342_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_27342_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: 157.812922 KDa |
Recombinant expression | Organism: ![]() |
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 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 |