+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11690 | |||||||||
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Title | Human TRPV4 structure in presence of 4a-PDD | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ion channel. open-conformation / agonist / 4a-PDD / 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 / regulation of response to osmotic stress / 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 / osmosensory signaling pathway / cellular hypotonic response / cellular hypotonic salinity response / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / cell volume homeostasis / cellular response to osmotic stress / positive regulation of monocyte chemotactic protein-1 production / calcium ion import / cell-cell junction assembly / TRP channels / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / diet induced thermogenesis / cytoplasmic microtubule / beta-tubulin binding / microtubule polymerization / alpha-tubulin binding / response to mechanical stimulus / monoatomic cation channel activity / SH2 domain binding / bioluminescence / actin filament organization / filopodium / generation of precursor metabolites and energy / calcium ion transmembrane transport / adherens junction / protein kinase C binding / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / ruffle membrane / positive regulation of interleukin-6 production / intracellular calcium ion homeostasis / positive regulation of inflammatory response / calcium ion transport / 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 / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Aequorea victoria (jellyfish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 Å | |||||||||
Authors | Botte M / Ulrich AKG | |||||||||
Citation | Journal: To Be Published Title: Cryo-EM structural studies of the agonist complexed human TRPV4 ion-channel reveals novel structural rearrangements resulting in an open-conformation Authors: Botte M / Ulrich AKG / Adaixo R / Gnutt D / Brockmann A / Bucher D / Chami M / Bocquet M / Ebbinghaus-Kintscher U / Puetter V / Becker A / Egner U / Stahlberg H / Hennig M / Holton SJ | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11690.map.gz | 481.5 MB | EMDB map data format | |
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Header (meta data) | emd-11690-v30.xml emd-11690.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_11690.png | 44.6 KB | ||
Filedesc metadata | emd-11690.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11690 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11690 | HTTPS FTP |
-Validation report
Summary document | emd_11690_validation.pdf.gz | 491.5 KB | Display | EMDB validaton report |
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Full document | emd_11690_full_validation.pdf.gz | 491.1 KB | Display | |
Data in XML | emd_11690_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_11690_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11690 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11690 | HTTPS FTP |
-Related structure data
Related structure data | 7aa5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11690.map.gz / Format: CCP4 / Size: 512 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: 0.639 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human TRPV4 in complex with 4a-PDD
Entire | Name: Human TRPV4 in complex with 4a-PDD |
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Components |
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-Supramolecule #1: Human TRPV4 in complex with 4a-PDD
Supramolecule | Name: Human TRPV4 in complex with 4a-PDD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 4,...
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Aequorea victoria (jellyfish) |
Molecular weight | Theoretical: 106.24182 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: MDYKDDDDKS SMGSRTSLYK KAGSLEVLFQ GPVFNRPILF DIVSRGSTAD LDGLLPFLLT HKKRLTDEEF REPSTGKTCL PKALLNLSN GRNDTIPVLL DIAERTGNMR EFINSPFRDI YYRGQTALHI AIERRCKHYV ELLVAQGADV HAQARGRFFQ P KDEGGYFY ...String: MDYKDDDDKS SMGSRTSLYK KAGSLEVLFQ GPVFNRPILF DIVSRGSTAD LDGLLPFLLT HKKRLTDEEF REPSTGKTCL PKALLNLSN GRNDTIPVLL DIAERTGNMR EFINSPFRDI YYRGQTALHI AIERRCKHYV ELLVAQGADV HAQARGRFFQ P KDEGGYFY FGELPLSLAA CTNQPHIVNY LTENPHKKAD MRRQDSRGNT VLHALVAIAD NTRENTKFVT KMYDLLLLKC AR LFPDSNL EAVLNNDGLS PLMMAAKTGK IGIFQHIIRR EVTDEDTRHL SRKFKDWAYG PVYSSLYDLS SLDTCGEEAS VLE ILVYNS KIENRHEMLA VEPINELLRD KWRKFGAVSF YINVVSYLCA MVIFTLTAYY QPLEGTPPYP YRTTVDYLRL AGEV ITLFT GVLFFFTNIK DLFMKKCPGV NSLFIDGSFQ LLYFIYSVLV IVSAALYLAG IEAYLAVMVF ALVLGWMNAL YFTRG LKLT GTYSIMIQKI LFKDLFRFLL VYLLFMIGYA SALVSLLNPC ANMKVCNEDQ TDCTVPTYPS CRDSETFSTF LLDLFK LTI GMGDLEMLSS TKYPVVFIIL LVTYIILTFV LLLNMLIALM GETVGQVSKE SKHIWKLQWA TTILDIERSF PVFLRKA FR SGEMVTVGKS SDGTPDRRWC FRVDEVNWSH ENLYFQGAAG SGEFKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGD A TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKRHDFFKSA MPEGYVQERT ISFKDDGNYK TRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN SHNVYITADK QKNGIKANFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQS ALSKDPNEKR DHMVLLEFVT AAGITHGMDE LYKASGHHHH HHHHHH UniProtKB: Transient receptor potential cation channel subfamily V member 4, Green fluorescent protein |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0533 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51215 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |