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- EMDB-35922: Agonist1 and Ruthenium Red bound state of mTRPV4 -

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Basic information

Entry
Database: EMDB / ID: EMD-35922
TitleAgonist1 and Ruthenium Red bound state of mTRPV4
Map data
Sample
  • Complex: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one
KeywordsmTRPV4 / STRUCTURAL PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


vasopressin secretion / regulation of response to osmotic stress / stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / hyperosmotic salinity response / calcium ion import into cytosol / cartilage development involved in endochondral bone morphogenesis / positive regulation of microtubule depolymerization / positive regulation of macrophage inflammatory protein 1 alpha production ...vasopressin secretion / regulation of response to osmotic stress / stretch-activated, monoatomic cation-selective, calcium channel activity / blood vessel endothelial cell delamination / osmosensor activity / hyperosmotic salinity response / calcium ion import into cytosol / cartilage development involved in endochondral bone morphogenesis / positive regulation of microtubule depolymerization / positive regulation of macrophage inflammatory protein 1 alpha production / positive regulation of striated muscle contraction / hypotonic response / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cellular hypotonic salinity response / cellular hypotonic response / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cortical microtubule organization / multicellular organismal-level water homeostasis / diet induced thermogenesis / calcium ion import / TRP channels / positive regulation of vascular permeability / positive regulation of monocyte chemotactic protein-1 production / negative regulation of brown fat cell differentiation / cell-cell junction assembly / osmosensory signaling pathway / cellular response to osmotic stress / response to osmotic stress / regulation of aerobic respiration / cortical actin cytoskeleton / positive regulation of macrophage chemotaxis / microtubule polymerization / calcium ion import across plasma membrane / energy homeostasis / alpha-tubulin binding / beta-tubulin binding / cytoplasmic microtubule / monoatomic cation channel activity / SH2 domain binding / protein kinase C binding / actin filament organization / filopodium / adherens junction / response to insulin / positive regulation of interleukin-6 production / intracellular calcium ion homeostasis / positive regulation of JNK cascade / ruffle membrane / calcium ion transmembrane transport / calcium channel activity / positive regulation of inflammatory response / calcium ion transport / actin filament binding / glucose homeostasis / negative regulation of neuron projection development / lamellipodium / cellular response to heat / positive regulation of cytosolic calcium ion concentration / growth cone / actin cytoskeleton organization / actin binding / cilium / microtubule binding / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / apical plasma membrane / focal adhesion / positive regulation of gene expression / lipid binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / ATP binding / metal ion binding / identical protein 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 / 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
Transient receptor potential cation channel subfamily V member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsZhen WX / Yang F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122040 China
CitationJournal: 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
DepositionApr 12, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35922.png

Downloads & links

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Map

FileDownload / File: emd_35922.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0746
Minimum - Maximum-0.34810495 - 0.58150053
Average (Standard dev.)0.00016069433 (±0.014855033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35922_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35922_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : mTRPV4 in complex with Agonist-1 and Ruthenium Red state

EntireName: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
Components
  • Complex: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
    • Protein or peptide: Transient receptor potential cation channel subfamily V member 4
  • Ligand: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one

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Supramolecule #1: mTRPV4 in complex with Agonist-1 and Ruthenium Red state

SupramoleculeName: mTRPV4 in complex with Agonist-1 and Ruthenium Red state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 75.666594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: 8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin...

MacromoleculeName: 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
Molecular weightTheoretical: 448.465 Da
Chemical component information

ChemComp-9QM:
8-fluoranyl-3-[4-(4-fluoranylphenoxy)phenyl]-2-(4-methylpiperazin-1-yl)quinazolin-4-one

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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

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 428608
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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