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- EMDB-11690: Human TRPV4 structure in presence of 4a-PDD -

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Basic information

Entry
Database: EMDB / ID: EMD-11690
TitleHuman TRPV4 structure in presence of 4a-PDD
Map data
Sample
  • Complex: Human TRPV4 in complex with 4a-PDD
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
  • Ligand: CALCIUM IONCalcium
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 / 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 / osmosensory signaling pathway / multicellular organismal-level water homeostasis / positive regulation of vascular permeability / cellular response to osmotic stress / calcium ion import / cell volume homeostasis / positive regulation of monocyte chemotactic protein-1 production / cell-cell junction assembly / TRP channels / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / beta-tubulin binding / diet induced thermogenesis / microtubule polymerization / alpha-tubulin binding / cytoplasmic microtubule / response to mechanical stimulus / monoatomic cation channel activity / SH2 domain binding / bioluminescence / protein kinase C binding / filopodium / generation of precursor metabolites and energy / actin filament organization / calcium ion transmembrane transport / adherens junction / positive regulation of JNK cascade / response to insulin / calcium channel activity / cilium / ruffle membrane / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / calcium ion transport / actin filament binding / glucose homeostasis / negative regulation of neuron projection development / lamellipodium / cellular response to heat / actin binding / growth cone / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / 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 / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 4 / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Transient receptor potential cation channel subfamily V member 4 / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Green fluorescent protein / Transient receptor potential cation channel subfamily V member 4
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsBotte M / Ulrich AKG / Adaixo R / Gnutt D / Brockmann A / Bucher D / Chami M / Bocquet M / Ebbinghaus-Kintscher U / Puetter V ...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
CitationJournal: 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
DepositionSep 3, 2020-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateAug 18, 2021-
Current statusAug 18, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.148
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.148
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aa5
  • Surface level: 0.148
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11690.png

Downloads & links

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Map

FileDownload / File: emd_11690.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.639 Å
Density
Contour LevelBy AUTHOR: 0.148 / Movie #1: 0.148
Minimum - Maximum-0.36322987 - 0.7391092
Average (Standard dev.)0.0021438804 (±0.025488673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 327.168 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6390.6390.639
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z327.168327.168327.168
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.3630.7390.002

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Supplemental data

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Sample components

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Entire : Human TRPV4 in complex with 4a-PDD

EntireName: Human TRPV4 in complex with 4a-PDD
Components
  • Complex: Human TRPV4 in complex with 4a-PDD
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Human TRPV4 in complex with 4a-PDD

SupramoleculeName: Human TRPV4 in complex with 4a-PDD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Macromolecule #1: Transient receptor potential cation channel subfamily V member 4,...

MacromoleculeName: Transient receptor potential cation channel subfamily V member 4,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 106.24182 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: 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

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0533 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51215

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