+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35918 | |||||||||
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Title | GSK101 and Ruthenium Red bound state of mTRPV4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mTRPV4 / STRUCTURAL PROTEIN / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / stretch-activated, monoatomic cation-selective, calcium channel activity / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response ...blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / stretch-activated, monoatomic cation-selective, calcium channel activity / positive regulation of striated muscle contraction / calcium ion import into cytosol / positive regulation of macrophage inflammatory protein 1 alpha production / negative regulation of brown fat cell differentiation / positive regulation of microtubule depolymerization / hyperosmotic salinity response / hypotonic response / cortical microtubule organization / positive regulation of chemokine (C-X-C motif) ligand 1 production / positive regulation of chemokine (C-C motif) ligand 5 production / cartilage development involved in endochondral bone morphogenesis / cellular hypotonic response / regulation of response to osmotic stress / cellular hypotonic salinity response / TRP channels / multicellular organismal-level water homeostasis / osmosensory signaling pathway / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / beta-tubulin binding / diet induced thermogenesis / cytoplasmic microtubule / microtubule polymerization / calcium ion import across plasma membrane / alpha-tubulin binding / monoatomic cation channel activity / energy homeostasis / SH2 domain binding / filopodium / actin filament organization / calcium ion transmembrane transport / protein kinase C binding / positive regulation of JNK cascade / adherens junction / calcium channel activity / response to insulin / cilium / ruffle membrane / positive regulation of inflammatory response / intracellular calcium ion homeostasis / positive regulation of interleukin-6 production / actin filament binding / lamellipodium / negative regulation of neuron projection development / glucose homeostasis / actin binding / cellular response to heat / positive regulation of cytosolic calcium ion concentration / growth cone / actin cytoskeleton organization / microtubule binding / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / response to hypoxia / apical plasma membrane / focal adhesion / lipid binding / positive regulation of gene expression / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / ATP binding / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
Authors | Zhen WX / Yang F | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2023 Title: Structural basis of ligand activation and inhibition in a mammalian TRPV4 ion channel. Authors: Wenxuan Zhen / Zhijun Zhao / Shenghai Chang / Xiaoying Chen / Yangzhuoqun Wan / Fan Yang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35918.map.gz | 52.4 MB | EMDB map data format | |
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Header (meta data) | emd-35918-v30.xml emd-35918.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
Images | emd_35918.png | 40.3 KB | ||
Filedesc metadata | emd-35918.cif.gz | 5.7 KB | ||
Others | emd_35918_half_map_1.map.gz emd_35918_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35918 | HTTPS FTP |
-Related structure data
Related structure data | 8j1bMC 8j1dC 8j1fC 8j1hC 8jkmC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35918.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35918_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35918_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GSK101 and Ruthenium Red bound state of mTRPV4
Entire | Name: GSK101 and Ruthenium Red bound state of mTRPV4 |
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Components |
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-Supramolecule #1: GSK101 and Ruthenium Red bound state of mTRPV4
Supramolecule | Name: GSK101 and Ruthenium Red bound state of mTRPV4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 4
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 4 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: 79.61168 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFAPAPQ PPPILKVFNR PILFDIVSRG STADLDGLLS FLLTHKKRLT DEEFREPST GKTCLPKALL NLSNGRNDTI PVLLDIAERT GNMREFINSP FRDIYYRGQT SLHIAIERRC KHYVELLVAQ G ADVHAQAR ...String: DYKDDDDKWS HPQFEKGGGG SGGSAWSHPQ FEKEFAPAPQ PPPILKVFNR PILFDIVSRG STADLDGLLS FLLTHKKRLT DEEFREPST GKTCLPKALL NLSNGRNDTI PVLLDIAERT GNMREFINSP FRDIYYRGQT SLHIAIERRC KHYVELLVAQ G ADVHAQAR GRFFQPKDEG GYFYFGELPL SLAACTNQPH IVNYLTENPH KKADMRRQDS RGNTVLHALV AIADNTRENT KF VTKMYDL LLLKCSRLFP DSNLETVLNN DGLSPLMMAA KTGKIGVFQH IIRREVTDED TRHLSRKFKD WAYGPVYSSL YDL SSLDTC GEEVSVLEIL VYNSKIENRH EMLAVEPINE LLRDKWRKFG AVSFYINVVS YLCAMVIFTL TAYYQPLEGT PPYP YRTTV DYLRLAGEVI TLFTGVLFFF TSIKDLFTKK CPGVNSLFVD GSFQLLYFIY SVLVVVSAAL YLAGIEAYLA VMVFA LVLG WMNALYFTRG LKLTGTYSIM IQKILFKDLF RFLLVYLLFM IGYASALVTL LNPCTNMKVC DEDQSNCTVP TYPACR DSE TFSAFLLDLF KLTIGMGDLE MLSSAKYPVV FILLLVTYII LTFVLLLNML IALMGETVGQ VSKESKHIWK LQWATTI LD IERSFPVFLR KAFRSGEMVT VGKSSDGTPD RRWCFRVDEV NWSHWNQNLG IINEDPGK UniProtKB: Transient receptor potential cation channel subfamily V member 4 |
-Macromolecule #2: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazi...
Macromolecule | Name: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide type: ligand / ID: 2 / Number of copies: 4 / Formula: XQ3 |
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Molecular weight | Theoretical: 655.613 Da |
Chemical component information | ChemComp-XQ3: |
-Macromolecule #3: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
Macromolecule | Name: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) type: ligand / ID: 3 / Number of copies: 1 / Formula: R2R |
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Molecular weight | Theoretical: 559.525 Da |
Chemical component information | ChemComp-R2R: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334401 |