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- EMDB-34301: Cryo-EM structure of the human TRPC5 ion channel in complex with ... -
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Open data
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Basic information
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Title | Cryo-EM structure of the human TRPC5 ion channel in complex with G alpha i3 subunits, class2 | |||||||||
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Function / homology | ![]() regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
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Method | ![]() ![]() | |||||||||
![]() | Won J / Jeong H / Lee HH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular architecture of the Gα-bound TRPC5 ion channel. Authors: Jongdae Won / Jinsung Kim / Hyeongseop Jeong / Jinhyeong Kim / Shasha Feng / Byeongseok Jeong / Misun Kwak / Juyeon Ko / Wonpil Im / Insuk So / Hyung Ho Lee / ![]() ![]() Abstract: G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated ...G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated that ion channels are direct effector molecules of the alpha subunit of G-proteins (Gα). However, no complete structural evidence supporting the direct interaction between Gα and ion channels is available. Here, we present the cryo-electron microscopy structures of the human transient receptor potential canonical 5 (TRPC5)-Gα complexes with a 4:4 stoichiometry in lipid nanodiscs. Remarkably, Gα binds to the ankyrin repeat edge of TRPC5 ~ 50 Å away from the cell membrane. Electrophysiological analysis shows that Gα increases the sensitivity of TRPC5 to phosphatidylinositol 4,5-bisphosphate (PIP), thereby rendering TRPC5 more easily opened in the cell membrane, where the concentration of PIP is physiologically regulated. Our results demonstrate that ion channels are one of the direct effector molecules of Gα proteins triggered by GPCR activation-providing a structural framework for unraveling the crosstalk between two major classes of transmembrane proteins: GPCRs and ion channels. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 81.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
Images | ![]() | 163 KB | ||
Others | ![]() ![]() | 117.9 MB 117.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gvxMC ![]() 7x6cC ![]() 7x6iC ![]() 8gvwC 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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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.088 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #2
File | emd_34301_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34301_additional_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Transient receptor potential
Entire | Name: Transient receptor potential![]() |
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Components |
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-Supramolecule #1: Transient receptor potential
Supramolecule | Name: Transient receptor potential / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Short transient receptor potential channel 5
Macromolecule | Name: Short transient receptor potential channel 5 / type: protein_or_peptide / ID: 1 Details: residues 766,767(SR) restriction enzyme, XbaI, residues 768-773(LEVLFQ) protease cleavage site, HRV-3C Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 89.951891 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI ...String: MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI PRPHQIRCNC VECVSSSEVD SLRHSRSRLN IYKALASPSL IALSSEDPIL TAFRLGWELK ELSKVENEFK AE YEELSQQ CKLFAKDLLD QARSSRELEI ILNHRDDHSE ELDPQKYHDL AKLKVAIKYH QKEFVAQPNC QQLLATLWYD GFP GWRRKH WVVKLLTCMT IGFLFPMLSI AYLISPRSNL GLFIKKPFIK FICHTASYLT FLFMLLLASQ HIVRTDLHVQ GPPP TVVEW MILPWVLGFI WGEIKEMWDG GFTEYIHDWW NLMDFAMNSL YLATISLKIV AYVKYNGSRP REEWEMWHPT LIAEA LFAI SNILSSLRLI SLFTANSHLG PLQISLGRML LDILKFLFIY CLVLLAFANG LNQLYFYYET RAIDEPNNCK GIRCEK QNN AFSTLFETLQ SLFWSVFGLL NLYVTNVKAR HEFTEFVGAT MFGTYNVISL VVLLNMLIAM MNNSYQLIAD HADIEWK FA RTKLWMSYFD EGGTLPPPFN IIPSPKSFLY LGNWFNNTFC PKRDPDGRRR RRNLRSFTER NADSLIQNQH YQEVIRNL V KRYVAAMIRN SKTHEGLTEE NFKELKQDIS SFRYEVLDLL GNRKSRLEVL FQ |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-3
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-3 type: protein_or_peptide / ID: 2 / Details: 6 histidine tag is inserted between M119 and T120. / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 41.399047 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AKEVKLLLLG AGESGKSTIV KQMKIIHEDG YSEDECKQYK VVVYSNTIQS IIAIIRAMG RLKIDFGEAA RADDARQLFV LAGSAEEGVM HHHHHHTPEL AGVIKRLWRD GGVQACFSRS REYQLNDSAS Y YLNDLDRI ...String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AKEVKLLLLG AGESGKSTIV KQMKIIHEDG YSEDECKQYK VVVYSNTIQS IIAIIRAMG RLKIDFGEAA RADDARQLFV LAGSAEEGVM HHHHHHTPEL AGVIKRLWRD GGVQACFSRS REYQLNDSAS Y YLNDLDRI SQSNYIPTQQ DVLRTRVKTT GIVETHFTFK DLYFKMFDVG GLRSERKKWI HCFEGVTAII FCVALSDYDL VL AEDEEMN RMHESMKLFD SICNNKWFTE TSIILFLNKK DLFEEKIKRS PLTICYPEYT GSNTYEEAAA YIQCQFEDLN RRK DTKEIY THFTCATDTK NVQFVFDAVT DVIIKNNLKE CGLY |
-Macromolecule #3: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PTY |
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Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ![]() ChemComp-PTY: |
-Macromolecule #4: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
Macromolecule | Name: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate type: ligand / ID: 7 / Number of copies: 4 / Formula: YZY |
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Molecular weight | Theoretical: 594.949 Da |
Chemical component information | ![]() ChemComp-YZY: |
-Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 4 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: OTHER Details: We combined two different maps from the same dataset (D_1300031718_em-additional-volume_P1.map.V4 and D_1300031718_em-additional-volume_P2.map.V4) to generate a composite map (D_1300031718_ ...Details: We combined two different maps from the same dataset (D_1300031718_em-additional-volume_P1.map.V4 and D_1300031718_em-additional-volume_P2.map.V4) to generate a composite map (D_1300031718_em-volume_P1.map.V6). The density of the G protein area could not be visualized clearly in the consensus map of this EM dataset. Therefore, we performed focused classification and local refinement to improve the density of the G protein area using symmetry expanded particles with C4 symmetry imposition, which required more number of particles. Finally, the number of particles used to reconstruct additional volume data 1 (D_1300031718_em-additional-volume_P1.map.V4) is 5,344 and the number of particles used to reconstruct additional volume data 2 (D_1300031718_em-additional-volume_P2.map.V4) is 205,343. Furthermore, the resolution stated above is based on map resolution estimates calculated by a validation tool in Phenix, FSC (model) = 0.143. Number images used: 5344 |