+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32436 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human TRPC5 channel in complex with riluzole | |||||||||||||||
Map data | sharpened map | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / Role of second messengers in netrin-1 signaling / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / Role of second messengers in netrin-1 signaling / negative regulation of dendrite morphogenesis / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding / positive regulation of axon extension / regulation of cytosolic calcium ion concentration / calcium channel complex / positive regulation of neuron differentiation / positive regulation of peptidyl-threonine phosphorylation / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / nervous system development / actin binding / positive regulation of cytosolic calcium ion concentration / ATPase binding / growth cone / neuron apoptotic process / neuronal cell body / dendrite / positive regulation of cell population proliferation / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||
Authors | Chen L / Wei M / Yang Y | |||||||||||||||
Funding support | China, 4 items
| |||||||||||||||
Citation | Journal: Cell Discov / Year: 2022 Title: Structural identification of riluzole-binding site on human TRPC5. Authors: Yaxiong Yang / Miao Wei / Lei Chen / | |||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_32436.map.gz | 164 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-32436-v30.xml emd-32436.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
Images | emd_32436.png | 142.1 KB | ||
Others | emd_32436_additional_1.map.gz emd_32436_additional_2.map.gz | 134.6 MB 134.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32436 | HTTPS FTP |
-Validation report
Summary document | emd_32436_validation.pdf.gz | 520.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_32436_full_validation.pdf.gz | 520.4 KB | Display | |
Data in XML | emd_32436_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_32436_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32436 | HTTPS FTP |
-Related structure data
Related structure data | 7wdbMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_32436.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.821 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: half map 1
File | emd_32436_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: half map 2
File | emd_32436_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : human transient receptor potential channel 5 tetramer
Entire | Name: human transient receptor potential channel 5 tetramer |
---|---|
Components |
|
-Supramolecule #1: human transient receptor potential channel 5 tetramer
Supramolecule | Name: human transient receptor potential channel 5 tetramer / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Short transient receptor potential channel 5
Macromolecule | Name: Short transient receptor potential channel 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 88.848578 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 GNR |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 4 / Formula: POV |
---|---|
Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: Y01 |
---|---|
Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA |
---|---|
Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine
Macromolecule | Name: 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine / type: ligand / ID: 6 / Number of copies: 4 / Formula: 657 |
---|---|
Molecular weight | Theoretical: 234.198 Da |
Chemical component information | ChemComp-657: |
-Macromolecule #7: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 7 / Number of copies: 4 / Formula: PTY |
---|---|
Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ChemComp-PTY: |
-Macromolecule #8: [3-[(~{E})-octadec-10-enoyl]oxy-2-oxidanyl-propyl] (~{E})-octadec...
Macromolecule | Name: [3-[(~{E})-octadec-10-enoyl]oxy-2-oxidanyl-propyl] (~{E})-octadec-10-enoate type: ligand / ID: 8 / Number of copies: 4 / Formula: 7OC |
---|---|
Molecular weight | Theoretical: 620.986 Da |
Chemical component information | ChemComp-7OC: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175028 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |