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- EMDB-28033: cryo-EM structure of TRPM3 ion channel in the presence with PIP2 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-28033
Titlecryo-EM structure of TRPM3 ion channel in the presence with PIP2 and PregS, state 2
Map dataTRPM3 in the presence of PIP2 and PregS, state 2, sharpened by a global B-factor of 121.5
Sample
  • Complex: TRPM3
    • Protein or peptide: Transient receptor potential cation channel, subfamily M, member 3
    • Protein or peptide: Unidentified segment at the N-terminus of TRPM3
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: [(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
  • Ligand: SODIUM ION
KeywordsTRPM3 / ion channel / PIP2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


zinc ion transmembrane transporter activity / zinc ion transmembrane transport / temperature-gated ion channel activity / sodium ion transport / monoatomic cation transport / monoatomic cation channel activity / phosphatidylinositol-4,5-bisphosphate binding / calcium channel activity / G-protein beta/gamma-subunit complex binding / calcium ion transmembrane transport ...zinc ion transmembrane transporter activity / zinc ion transmembrane transport / temperature-gated ion channel activity / sodium ion transport / monoatomic cation transport / monoatomic cation channel activity / phosphatidylinositol-4,5-bisphosphate binding / calcium channel activity / G-protein beta/gamma-subunit complex binding / calcium ion transmembrane transport / protein homotetramerization / calmodulin binding / plasma membrane
Similarity search - Function
TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / : / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao C / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionSep 3, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28033.png

Downloads & links

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Map

FileDownload / File: emd_28033.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRPM3 in the presence of PIP2 and PregS, state 2, sharpened by a global B-factor of 121.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.5948294 - 2.6618044
Average (Standard dev.)-0.00091615296 (±0.06909632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: TRPM3 in the presence of PIP2 and PregS, state 2, half-map 2

Fileemd_28033_half_map_1.map
AnnotationTRPM3 in the presence of PIP2 and PregS, state 2, half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TRPM3 in the presence of PIP2 and PregS, state 2, half-map 1

Fileemd_28033_half_map_2.map
AnnotationTRPM3 in the presence of PIP2 and PregS, state 2, half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPM3

EntireName: TRPM3
Components
  • Complex: TRPM3
    • Protein or peptide: Transient receptor potential cation channel, subfamily M, member 3
    • Protein or peptide: Unidentified segment at the N-terminus of TRPM3
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: [(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
  • Ligand: SODIUM ION

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Supramolecule #1: TRPM3

SupramoleculeName: TRPM3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Transient receptor potential cation channel, subfamily M, member 3

MacromoleculeName: Transient receptor potential cation channel, subfamily M, member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 154.649328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Unidentified segment at the N-terminus of TRPM3

MacromoleculeName: Unidentified segment at the N-terminus of TRPM3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.464797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #4: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 4 / Number of copies: 4 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #5: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(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
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(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

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Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.865 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152184
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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