+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35922 | |||||||||
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Title | Agonist1 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 stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / 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 ...stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / vasopressin secretion / 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 / regulation of response to osmotic stress / 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 / cellular hypotonic salinity response / multicellular organismal-level water homeostasis / TRP channels / osmosensory signaling pathway / positive regulation of vascular permeability / cellular response to osmotic stress / positive regulation of monocyte chemotactic protein-1 production / calcium ion import / cell-cell junction assembly / response to osmotic stress / cortical actin cytoskeleton / regulation of aerobic respiration / positive regulation of macrophage chemotaxis / diet induced thermogenesis / cytoplasmic microtubule / beta-tubulin binding / microtubule polymerization / alpha-tubulin binding / monoatomic cation channel activity / energy homeostasis / SH2 domain binding / actin filament organization / filopodium / adherens junction / calcium ion transmembrane transport / protein kinase C binding / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / positive regulation of interleukin-6 production / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / actin filament binding / negative regulation of neuron projection development / lamellipodium / glucose homeostasis / actin binding / cellular response to heat / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / growth cone / microtubule binding / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / calmodulin binding / 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: 3.88 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_35922.map.gz | 51.8 MB | EMDB map data format | |
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Header (meta data) | emd-35922-v30.xml emd-35922.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_35922.png | 45 KB | ||
Filedesc metadata | emd-35922.cif.gz | 5.5 KB | ||
Others | emd_35922_half_map_1.map.gz emd_35922_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35922 | HTTPS FTP |
-Validation report
Summary document | emd_35922_validation.pdf.gz | 886.3 KB | Display | EMDB validaton report |
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Full document | emd_35922_full_validation.pdf.gz | 885.8 KB | Display | |
Data in XML | emd_35922_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_35922_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35922 | HTTPS FTP |
-Related structure data
Related structure data | 8j1hMC 8j1bC 8j1dC 8j1fC 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_35922.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: #1
File | emd_35922_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35922_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : mTRPV4 in complex with Agonist-1 and Ruthenium Red state
Entire | Name: mTRPV4 in complex with Agonist-1 and Ruthenium Red state |
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Components |
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-Supramolecule #1: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
Supramolecule | Name: mTRPV4 in complex with Agonist-1 and Ruthenium Red state 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: 75.666594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: APAPQPPPIL KVFNRPILFD IVSRGSTADL DGLLSFLLTH KKRLTDEEFR EPSTGKTCLP KALLNLSNGR NDTIPVLLDI AERTGNMRE FINSPFRDIY YRGQTSLHIA IERRCKHYVE LLVAQGADVH AQARGRFFQP KDEGGYFYFG ELPLSLAACT N QPHIVNYL ...String: APAPQPPPIL KVFNRPILFD IVSRGSTADL DGLLSFLLTH KKRLTDEEFR EPSTGKTCLP KALLNLSNGR NDTIPVLLDI AERTGNMRE FINSPFRDIY YRGQTSLHIA IERRCKHYVE LLVAQGADVH AQARGRFFQP KDEGGYFYFG ELPLSLAACT N QPHIVNYL TENPHKKADM RRQDSRGNTV LHALVAIADN TRENTKFVTK MYDLLLLKCS RLFPDSNLET VLNNDGLSPL MM AAKTGKI GVFQHIIRRE VTDEDTRHLS RKFKDWAYGP VYSSLYDLSS LDTCGEEVSV LEILVYNSKI ENRHEMLAVE PIN ELLRDK WRKFGAVSFY INVVSYLCAM VIFTLTAYYQ PLEGTPPYPY RTTVDYLRLA GEVITLFTGV LFFFTSIKDL FTKK CPGVN SLFVDGSFQL LYFIYSVLVV VSAALYLAGI EAYLAVMVFA LVLGWMNALY FTRGLKLTGT YSIMIQKILF KDLFR FLLV YLLFMIGYAS ALVTLLNPCT NMKVCDEDQS NCTVPTYPAC RDSETFSAFL LDLFKLTIGM GDLEMLSSAK YPVVFI LLL VTYIILTFVL LLNMLIALMG ETVGQVSKES KHIWKLQWAT TILDIERSFP VFLRKAFRSG EMVTVGKSSD GTPDRRW CF RVDEVNWSHW NQNLGIINED PGK UniProtKB: Transient receptor potential cation channel subfamily V member 4 |
-Macromolecule #2: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin...
Macromolecule | Name: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one type: ligand / ID: 2 / Number of copies: 4 / Formula: 9QM |
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Molecular weight | Theoretical: 448.465 Da |
Chemical component information | ChemComp-9QM: |
-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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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 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: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 428608 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |